Fluorogenic pH-Sensitive Dyes and Their Methods of Use

ABSTRACT

Disclosed herein are compounds, compositions, methods and kits for detecting pH in samples using pH-sensitive fluorescent dyes. The compounds disclosed herein are novel xanthene-derivative dyes comprising an aniline moiety with one or more electron donating groups, which dyes are for detecting pH in samples either in vitro or in vivo. Also described herein are processes for preparing said dyes for use in the disclosed compositions, methods and kits.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of priority to U.S. ProvisionalApplication Ser. Nos. 61/653,333, filed May 30, 2012 and 61/653,616,filed May 31, 2012, which are herein incorporated by reference in theirentirety.

FIELD

Novel pH-sensitive fluorescent dyes and assays for use in a variety ofapplications including monitoring of intracellular processes aredisclosed.

BACKGROUND

pH-sensitive fluorescent dyes employed in biological research andmedical diagnostics belong to two groups, each distinguished by theorigin of fluorescent responses to changes in pH. The first groupincludes compounds having fluorescence controlled by the ionization ofphenolic hydroxyl groups in a fluorophore. Examples include fluorescein,carboxyfluorescein, Oregon Green®, SNARF®, SNAFL®, and HPTS indicators.

U.S. Patent Publication No. 2006/0051874 describes fluorescein-likestructures incorporated into a fluorescent detector for monitoring pH ofthe blood in bank storages. Because the degree of ionization of thesetypes of molecules increases upon lowering the acidity of theenvironment, they become more fluorescent as pH increases.

Fluorescent pH sensors of the second group include an amino group(aliphatic or aromatic) as an indicator moiety along with a reporterfluorescent dye moiety. When such a molecule absorbs a photon creatingan excited electronic state, the electron of the amino group's unsharedpair transfers to the orbital vacated by excitation. Such an electrontransfer, referred to as Photoinduced Electron Transfer (PET) preventsthe excited molecule from emission transition, thus the fluorescence ofthe dye is quenched. Protonation of the amino group changes the natureand energy of the pair's orbital and stops the PET. As a result, thefluorescent reporter moiety responds to a pH change. Because protonationof the amino group cancels the quenching, the PET-based sensors becomemore fluorescent as pH decreases.

Examples of PET-based pH sensors include LysoSensor™ dyes, which containa dimethylamino group as an indicator moiety and CypHer® 5E dye whichhas an indolenine indicator group. One disadvantage of these sensors isthat the working range is shifted to the acidic side because of the lowpKa of the indicator amino group.

A family of rhodamine-based pH sensors is described in PCT PublicationNo. WO 2005/098437 (Smith et al.). The dyes have a benzene ringsubstituted ortho to the xanthene moiety by —OH or —SH (or theirdeprotonated forms), such that deprotonation to a negatively chargedstate quenches the fluorescence and it is only upon protonation of thenegatively charged O⁻ or S⁻ to a neutral state that the fluorescence isrestored. Typically, the pH at which this occurs is less than pH 6. WO2005/098437 purports that the ionized state of the —OH or —SH group isresponsible for the pH response of the dye and that the strong electronwithdrawing properties of the tetramethylrhodamine moiety in the dyessignificantly decreases the pKa of the indicator group, thus shiftingthe sensors' working range toward highly acidic pH values. However, thislimits the applicability of the dyes described in WO 2005/098437 at aphysiological pH (e.g., pH 6-7), especially in biological systems. Anadditional disadvantage of these dyes is that their pKa is not tunable.Furthermore, these compounds have been found by us to be unstable insolution.

Accordingly, there is a need for additional pH sensitive fluorescentdyes with improved properties, including in at least some compounds theability to detect pH changes in biological systems. It is an object ofthe present invention to develop a novel class of relatively stablefluorescent pH sensors that fluoresce in the green portion of the UV/VISspectrum, preferably with a working range towards neutral and otherbiologically relevant pH values that mitigate or remove thedisadvantages of the compounds known in art.

SUMMARY

Described herein are compounds, compositions, methods and kits fordetecting pH in samples using pH-sensitive fluorescent dyes, which inone aspect, are characterized by the omission of a hydroxyl or thiolgroup as required by WO 2005/098437. In another aspect, the pH-sensitivefluorescent dyes as disclosed herein allow for the detection offluorescent responses to changes in pH in the green portion of theUV/VIS spectrum. The current disclosure provides a new family ofpH-sensitive green fluorescent dyes, having significant and unexpectedadvantages over existing fluorescent pH-sensors in that the presence ofa dialkylamino group para to the alkoxy substituent results inphysiological pKa values and the pKa's of the dyes provided herein arealso tunable. Therefore, the pH-sensitive fluorescent dyes providedherein may be modified to suit a particular application or condition tobe analyzed.

In certain embodiments, novel dye compounds are provided for use asfluorescent pH sensors, the dye compounds having structural formula (I):

wherein

R¹ is alkoxy or thioalkyl;

R² and R⁶, which may be the same or different, are each independently H,halogen, —OR^(a), —SR^(a), —NR^(a)R^(b), or an electron donating group;

R³ is —NR′R″, wherein R′ and R″, which may be the same or different, areeach independently alkyl or substituted alkyl;

R⁴ is selected from the group consisting of alkyl and substituted alkyl;

R⁵ is selected from the group consisting of alkyl; substituted alkyl;alkenyl; substituted alkenyl; acyl; aryl; substituted aryl;carboxyalkyl; heteroaryl; substituted heteroaryl; heterocyclyl;substituted heterocyclyl; alkylcarboxy; alkylalkoxycarbonyl;alkylaminocarbonyl; alkylaryloxycarbonyl; alkylheteroaryl; (CH₂)CO(O)R;(CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NRR^(c); wherein n is aninteger from 1 to 6, and R and R^(c), which may be the same ordifferent, are each independently H, alkyl, substituted alkyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, substituted amino,alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilic group,or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR, wherein n is an integerfrom 1 to 6, and R_(x) is a reactive group; -L-R_(x); and -L-S_(c),wherein L is a linker, R_(x) is a reactive group, and S_(c) is aconjugated substance;

R^(a) is H, alkyl, or substituted alkyl; and

R^(b) is alkyl or substituted alkyl.

In certain embodiments, R¹-R⁶ are as follows:

R¹ is alkoxy or thioalkyl;

R² and R⁶, which may be the same or different, are each independently Hor halogen;

R³ is —NR′R″, wherein R′ and R″, which may be the same or different, areeach independently alkyl;

R⁴ is alkyl; and

R⁵ is selected from the group consisting of alkyl; substituted alkyl;alkenyl; substituted alkenyl; acyl; aryl; substituted aryl;carboxyalkyl; heteroaryl; substituted heteroaryl; heterocyclyl;substituted heterocyclyl; alkylcarboxy; alkylalkoxycarbonyl;alkylaminocarbonyl; alkylaryloxycarbonyl; alkylheteroaryl;(CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NRR^(c);wherein n is an integer from 1 to 6, and R and R^(c), which may be thesame or different, are each independently H, alkyl, substituted alkyl,aryl, substituted aryl, heteroaryl, substituted heteroaryl, substitutedamino, alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilicgroup, or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is aninteger from 1 to 6, and R_(x) is a reactive group; -L-R_(x); and-L-S_(c).

In certain embodiments, R¹-R⁶ are as follows:

R¹ is alkoxy or thioalkyl;

R² and R⁶, which may be the same or different, are each independently H,Cl or F;

R³ is —NR′R″, wherein R′ and R″, which may be the same or different, areeach independently alkyl;

R⁴ is alkyl; and

R⁵ is selected from the group consisting of alkyl; substituted alkyl;alkenyl; substituted alkenyl; acyl; aryl; substituted aryl;carboxyalkyl; heteroaryl; substituted heteroaryl; heterocyclyl;substituted heterocyclyl; alkylcarboxy; alkylalkoxycarbonyl;alkylaminocarbonyl; alkylaryloxycarbonyl; alkylheteroaryl;(CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NRR^(c);wherein n is an integer from 1 to 6, and R and R^(c), which may be thesame or different, are each independently H, alkyl, substituted alkyl,aryl, substituted aryl, heteroaryl, substituted heteroaryl, substitutedamino, alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilicgroup, or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is aninteger from 1 to 6, and R_(x) is a reactive group; -L-R_(x); and-L-S_(c).

In certain embodiments, R¹-R⁶ are as follows:

R¹ is alkoxy or thioalkyl;

R² and R⁶ are each H;

R³ is —NR′R″, wherein R′ and R″, which may be the same or different, areeach independently alkyl;

R⁴ is alkyl; and

R⁵ is selected from the group consisting of alkyl; substituted alkyl;alkenyl; substituted alkenyl; acyl; aryl; substituted aryl;carboxyalkyl; heteroaryl; substituted heteroaryl; heterocyclyl;substituted heterocyclyl; alkylcarboxy; alkylalkoxycarbonyl;alkylaminocarbonyl; alkylaryloxycarbonyl; alkylheteroaryl;(CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NRR^(c);wherein n is an integer from 1 to 6, and R and R^(c), which may be thesame or different, are each independently H, alkyl, substituted alkyl,aryl, substituted aryl, heteroaryl, substituted heteroaryl, substitutedamino, alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilicgroup, or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR, wherein n is aninteger from 1 to 6, and R_(x) is a reactive group; -L-R_(x); and-L-S_(c),

In certain embodiments, R₁-R⁶ are as follows:

R₁ is methoxy;

R² and R⁶ are each H;

R³ is —NR′R″, wherein R′ and R″, which may be the same or different, areeach independently methyl or ethyl;

R⁴ is methyl or ethyl; and

R⁵ is methyl; ethyl; carboxyalkyl; (CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R;(CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NRR^(c); wherein n is an integer from 1to 6, and R and R^(c), which may be the same or different, are eachindependently H, alkyl, substituted alkyl, aryl, substituted aryl,heteroaryl, substituted heteroaryl, substituted amino,alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilic group,or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is an integerfrom 1 to 6, and R_(x) is a reactive group selected from carboxyl,carboxylester, amide, maleimide, succinimidyl ester (SE),sulfodichlorophenol (SDP) ester, sulfotetrafluorophenol (STP) ester,tetrafluorophenol (TFP) ester, acetoxymethoxy (AM) ester,nitrilotriacetic acid (NTA), aminodextran, DIBO-amine; -L-R_(x); or-L-S_(c).

In certain embodiments, novel dye compounds are provided for use asfluorescent pH sensors, the dye compounds having structural formula(II):

wherein

R₁ is alkoxy or thioalkyl;

R² and R⁶, which may be the same or different, are each independently H,halogen, —OR^(a), —SR^(a), —NR^(a)R^(b), or an electron donating group;

R³ is —NR′R″, wherein R′ and R″, which may be the same or different, areeach independently alkyl or substituted alkyl;

R⁴ is selected from the group consisting of alkyl and substituted alkyl;

R⁵ is selected from the group consisting of alkyl; substituted alkyl;alkenyl; substituted alkenyl; acyl; aryl; substituted aryl;carboxyalkyl; heteroaryl; substituted heteroaryl; heterocyclyl;substituted heterocyclyl; alkylcarboxy; alkylalkoxycarbonyl;alkylaminocarbonyl; alkylaryloxycarbonyl; alkylheteroaryl;(CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NRR^(c);wherein n is an integer from 1 to 6, and R and R^(c), which may be thesame or different, are each independently H, alkyl, substituted alkyl,aryl, substituted aryl, heteroaryl, substituted heteroaryl, substitutedamino, alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilicgroup, or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR, wherein n is aninteger from 1 to 6, and R_(x) is a reactive group; -L-R_(x); and-L-S_(c), wherein L is a linker, R_(x) is a reactive group, and S_(c) isa conjugated substance;

R^(a) is H, alkyl, or substituted alkyl; and

R^(b) is alkyl or substituted alkyl.

In certain embodiments, R₁-R⁶ are as follows:

R₁ is alkoxy or thioalkyl;

R² and R⁶, which may be the same or different, are each independently Hor halogen;

R³ is —NR′R″, wherein R′ and R″, which may be the same or different, areeach independently alkyl;

R⁴ is alkyl; and

R⁵ is selected from the group consisting of alkyl; substituted alkyl;alkenyl; substituted alkenyl; acyl; aryl; substituted aryl;carboxyalkyl; heteroaryl; substituted heteroaryl; heterocyclyl;substituted heterocyclyl; alkylcarboxy; alkylalkoxycarbonyl;alkylaminocarbonyl; alkylaryloxycarbonyl; alkylheteroaryl;(CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NRR^(c);wherein n is an integer from 1 to 6, and R and R^(c), which may be thesame or different, are each independently H, alkyl, substituted alkyl,aryl, substituted aryl, heteroaryl, substituted heteroaryl, substitutedamino, alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilicgroup, or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR, wherein n is aninteger from 1 to 6, and R_(x) is a reactive group; -L-R_(x); and-L-S_(c).

In certain embodiments, R₁-R⁶ are as follows:

R₁ is alkoxy or thioalkyl;

R² and R⁶, which may be the same or different, are each independently H,Cl or F;

R³ is —NR′R″, wherein R′ and R″, which may be the same or different, areeach independently alkyl;

R⁴ is alkyl; and

R⁵ is selected from the group consisting of alkyl; substituted alkyl;alkenyl; substituted alkenyl; acyl; aryl; substituted aryl;carboxyalkyl; heteroaryl; substituted heteroaryl; heterocyclyl;substituted heterocyclyl; alkylcarboxy; alkylalkoxycarbonyl;alkylaminocarbonyl; alkylaryloxycarbonyl; alkylheteroaryl;(CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NNR^(c);wherein n is an integer from 1 to 6, and R and R^(c), which may be thesame or different, are each independently H, alkyl, substituted alkyl,aryl, substituted aryl, heteroaryl, substituted heteroaryl, substitutedamino, alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilicgroup, or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is aninteger from 1 to 6, and R_(x) is a reactive group; -L-R_(x); and-L-S_(c).

In certain embodiments, R₁-R⁶ are as follows:

R₁ is alkoxy or thioalkyl;

R² and R⁶ are each H;

R³ is —NR′R″, wherein R′ and R″, which may be the same or different, areeach independently alkyl;

R⁴ is alkyl; and

R⁵ is selected from the group consisting of alkyl; substituted alkyl;alkenyl; substituted alkenyl; acyl; aryl; substituted aryl;carboxyalkyl; heteroaryl; substituted heteroaryl; heterocyclyl;substituted heterocyclyl; alkylcarboxy; alkylalkoxycarbonyl;alkylaminocarbonyl; alkylaryloxycarbonyl; alkylheteroaryl;(CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NNR^(c);wherein n is an integer from 1 to 6, and R and R^(c), which may be thesame or different, are each independently H, alkyl, substituted alkyl,aryl, substituted aryl, heteroaryl, substituted heteroaryl, substitutedamino, alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilicgroup, or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is aninteger from 1 to 6, and R_(x) is a reactive group; -L-R_(x); and-L-S_(c).

In certain embodiments, R₁-R⁶ are as follows:

R₁ is methoxy;

R² and R⁶ are each H;

R³ is —NR′R″, wherein R′ and R″, which may be the same or different, areeach independently methyl or ethyl;

R⁴ is methyl or ethyl; and

R⁵ is methyl; ethyl; carboxyalkyl; (CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R;(CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NRR^(c); wherein n is an integer from 1to 6, and R and R^(c), which may be the same or different, are eachindependently H, alkyl, substituted alkyl, aryl, substituted aryl,heteroaryl, substituted heteroaryl, substituted amino,alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilic group,or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is an integerfrom 1 to 6, and R_(x) is a reactive group selected from carboxyl,carboxylester, amide, maleimide, succinimidyl ester (SE),sulfodichlorophenol (SDP) ester, sulfotetrafluorophenol (STP) ester,tetrafluorophenol (TFP) ester, acetoxymethoxy (AM) ester,nitrilotriacetic acid (NTA), aminodextran, DIBO-amine; -L-R_(x); or-L-S_(c).

In certain embodiments, compositions are provided for determining the pHof a sample, the compositions comprising:

a) one or more of the pH-sensitive fluorescent dye compounds describedherein; and

b) a carrier,

wherein the one or more pH-sensitive fluorescent dye compounds arepresent in an amount effective to detect the pH of the sample.

In certain embodiments, compositions are provided for determining the pHof a sample, the compositions comprising:

(a) one or more of the pH-sensitive fluorescent dye compounds describedherein; and

(b) an analyte,

wherein the one or more pH-sensitive fluorescent dye compounds arepresent in an amount effective to detect the pH of the sample.

In certain embodiments, methods are provided for determining the pH of asample, the methods comprising:

(a) contacting the sample with one or more of the pH-sensitivefluorescent dye compounds described herein to form a contacted sample;

(b) incubating the contacted sample for an appropriate amount of time toform an incubated sample;

(c) illuminating the incubated sample with an appropriate wavelength toform an illuminated sample; and

(d) detecting fluorescent emissions from the illuminated sample;

wherein the fluorescent emissions are used to determine the pH of thesample.

In certain embodiments, methods are provided for determining the pH of asample, the methods comprising:

(a) contacting the sample with one or more of the compositions describedherein to form a contacted sample;

(b) incubating the contacted sample for an appropriate amount of time toform an incubated sample;

(c) illuminating the incubated sample with an appropriate wavelength toform an illuminated sample; and

(d) detecting fluorescent emissions from the illuminated sample;

wherein the fluorescent emissions are used to determine the pH of thesample.

In certain embodiments, methods are provided for monitoring the pHinside a live cell, the methods comprising:

(a) contacting the cell with one or more of the pH-sensitive fluorescentdye compounds described herein to form a contacted cell;

(b) incubating the contacted cell for a sufficient amount of time forthe one or more pH-sensitive fluorescent dye compounds to enter the cellto form a labeled cell;

(c) illuminating the labeled cell with an appropriate wavelength to forman illuminated cell; and

(d) detecting fluorescent emissions from the illuminated cell;

wherein the fluorescent emissions are used to monitor the pH inside thecell.

In certain embodiments, methods are provided for monitoring the pHinside a live cell, the methods comprising:

(a) contacting the cell with one or more of the compositions describedherein to form a contacted cell;

(b) incubating the contacted cell for a sufficient amount of time forthe one or more compositions to enter the cell to form a labeled cell;

(c) illuminating the labeled cell with an appropriate wavelength to forman illuminated cell; and

(d) detecting fluorescent emissions from the illuminated cell;

wherein the fluorescent emissions are used to monitor the pH inside thecell.

In certain embodiments, methods are provided for detecting phagocytosisof a carrier molecule in solution, the methods comprising:

(a) conjugating the carrier molecule to one or more of the pH-sensitivefluorescent dye compounds described herein to form a carrier-dyeconjugate;

(b) contacting the carrier-dye conjugate with a cell to form a contactedcell;

(c) incubating the contacted cell to form an incubated solution;

(d) illuminating the incubated solution to form an illuminated solution;and

(e) detecting fluorescent emissions from the illuminated solution;

wherein fluorescent emissions indicate phagocytosis of the carriermolecule.

In certain embodiments, methods are provided for detecting phagocytosisof a carrier molecule in solution, the methods comprising:

(a) conjugating the carrier molecule to one or more of the compositionsdescribed herein to form a carrier-dye conjugate;

(b) contacting the carrier-dye conjugate with a cell to form a contactedcell;

(c) incubating the contacted cell to form an incubated solution;

(d) illuminating the incubated solution to form an illuminated solution;and

(e) detecting fluorescent emissions from the illuminated solution;

wherein fluorescent emissions indicate phagocytosis of the carriermolecule.

In certain embodiments, methods are provided for detecting a pH relatedintracellular process, the methods comprising:

(a) contacting any one of the pH-sensitive fluorescent dye compoundsdescribed herein with a cell to form a contacted cell;

(b) incubating the contacted cell to form an incubated solution;

(c) illuminating the incubated solution to form an illuminated solution;and

(d) detecting fluorescent emissions from the illuminated solution;

wherein increased fluorescent emissions indicates activation of theintracellular process.

In certain embodiments, methods are provided for detecting a pH relatedintracellular process, the methods comprising:

(a) contacting any one of the compositions described herein with a cellto form a contacted cell;

(b) incubating the contacted cell to form an incubated solution;

(c) illuminating the incubated solution to form an illuminated solution;and

(d) detecting fluorescent emissions from the illuminated solution;

wherein increased fluorescent emissions indicates activation of theintracellular process.

In certain embodiments, methods are provided for identifying a targetcell in a population of cells, wherein the target cell is differentiallylabeled relative to neighboring cells within the population, the methodscomprising;

(a) contacting one or more of the pH-sensitive dye compounds disclosedherein with the population of cells to form a contacted cell population;

(b) incubating the contacted cell population for a period of timesufficient for the one or more of the pH-sensitive dye compounds toenter the target cell, thereby forming an incubated cell population; and

(c) illuminating the incubated cell population, wherein the target cellis identified by a differential label relative to neighboring cellswithin the population.

In certain embodiments, methods are provided for identifying a targetcell in a population of cells, wherein the target cell is differentiallylabeled relative to neighboring cells within the population, the methodscomprising;

(a) contacting one or more of the compositions disclosed herein with thepopulation of cells to form a contacted cell population;

(b) incubating the contacted cell population for a period of timesufficient for the one or more of the compositions to enter the targetcell, thereby forming an incubated cell population; and

(c) illuminating the incubated cell population, wherein the target cellis identified by a differential label relative to neighboring cellswithin the population.

In certain embodiments, methods are provided for diagnosing or detectinga disease in a subject, the method comprising:

(a) contacting a sample obtained from a subject suspected of having thedisease with one or more of the pH-sensitive dye compounds disclosedherein to form a contacted sample;

(b) incubating the contacted sample for an appropriate amount of time toform an incubated sample;

(c) illuminating the incubated sample with an appropriate wavelength toform an illuminated sample; and

(d) detecting fluorescent emissions from the illuminated sample;

wherein the fluorescent emissions are used to diagnose or detect thedisease.

In certain embodiments, methods are provided for diagnosing or detectinga disease in a subject, the methods comprising:

(a) contacting a sample obtained from a subject suspected of having thedisease with one or more of the compositions disclosed herein to form acontacted sample;

(b) incubating the contacted sample for an appropriate amount of time toform an incubated sample;

(c) illuminating the incubated sample with an appropriate wavelength toform an illuminated sample; and

(d) detecting fluorescent emissions from the illuminated sample;

wherein the fluorescent emissions are used to diagnose or detect thedisease.

In certain embodiments, kits are provided for determining the pH of asample comprising:

(a) one or more of the pH-sensitive fluorescent dye compounds describedherein;

(b) one or more containers; and optionally

(c) instructions for determining the pH of the sample.

In certain embodiments, kits are provided for determining the pH of asample comprising:

(a) one or more of the compositions described herein;

(b) one or more containers; and optionally

(c) instructions for determining the pH of the sample.

In certain embodiments processes are provided for synthesizing acompound of structural formula (I):

the process comprising:

-   -   a) contacting a compound of structural formula (VI):

-   -   with a compound of structural formula (IV):

-   -   to form a compound of structural formula (VII):

-   -   b) de-allylating the compound of structural formula (VII), when        R⁷, R⁸, R⁹ and R₁₀ are each allyll, to form a compound of        structural formula (I),

wherein R¹, R², R³, R⁴, R⁵, R⁶ are as previously defined herein.

In certain embodiments, processes are provided of synthesizing acompound of structural formula (II):

the process comprising:

-   -   a) contacting a compound of structural formula (III):

-   -   with a compound of structural formula (IV):

-   -   to form a compound of structural formula (V):

-   -   b) de-allylating the compound of structural formula (V), when R⁷        and R⁸ are each allyl, to form a compound of structural formula        (II),

wherein R¹, R², R³, R⁴, R⁵ and R⁶ are as previously defined herein.

Other embodiments and illustrative aspects, features and advantages ofthe present invention will become apparent from the following detaileddescription. It should be understood, however, that the detaileddescription and the specific examples, while indicating preferredembodiments, are given by way of illustration only, since variouschanges and modifications within the spirit and scope of the presentinvention will become apparent to those skilled in the art from thisdetailed description.

BRIEF DESCRIPTION OF THE FIGURES

Although the following figures depict various examples of the invention,the invention is not limited to the examples depicted in the figures.

FIG. 1 is a schematic representation of the pH values for intracellularcompartments and organelles.

FIG. 2 describes cellular uptake of pH-sensitive fluorescent dyecompounds. Panel A is a schematic representation of cellular uptake ofpH-sensitive fluorescent dye-conjugated compounds includingdye-conjugated bacteria for monitoring phagocytosis and dye-conjugatedparticles for monitoring endocytosis, using the compounds and methodsaccording to embodiments disclosed herein. Panel B is a fluorescencemicrograph showing cells that have taken up a pH-sensitive fluorescentdye-conjugated compound according to certain embodiments of the presentteachings.

FIG. 3 graphically shows the correlation of pH with fluorescence forCompound (1). Panel A shows the fluorescence intensity of Compound (1)as a function of pH. Panel B shows the pKa of Compound (1).

FIG. 4 graphically shows the correlation of pH with fluorescence forCompound (2). Panel A shows the fluorescence intensity of Compound (2)as a function of pH. Panel B shows the pKa of Compound (2).

FIG. 5 graphically shows the correlation of pH with fluorescence forCompound (3). Panel A shows the fluorescence intensity of Compound (3)as a function of pH. Panel B shows the pKa of Compound (3).

FIG. 6 shows a micrograph of phagocytic uptake of pH-sensitivefluorescent dye-conjugated E. coli, Staphylococcus, and zymosan (yeast)bioparticles of RAW cells.

FIG. 7 graphically shows a dose response curve of cytochalasin Dinhibition of Compound (1)-conjugated bioparticles internalization in ahigh-throughput microplate-based assay using cultured macrophage “MMM”cells.

FIGS. 8A and 8B show fluorescent pH sensor dye uptake. FIG. 8A shows aseries of pH curves for E. coli bioparticles labeled with Compound (2),Compound (12) and Compound (28), emphasizing their relative responses toacidification in vitro. FIG. 8B shows a false-color fluorescence rangefor E. coli labeled with Compound (2), Compound (12) or Compound (28)and resuspended in solutions of varying pH (pH 4-pH 8.5).

FIG. 9 shows a graphic representation of the relative fluorescenceincrease with acidification of 10,000 MW dextran labeled with Compound(22).

FIG. 10 shows a graphic representation of the pH response (relativefluorescence vs. pH) of a goat-anti-mouse (GAM) antibody labeled with anamine-reactive (maleimide) Compound (24). The triangle line is Compound(24)-GAM MR 10 DOS 2 and the square line is Compound (24)-GAM MR 20 DOS1.8.

FIG. 11 shows a graphic representation of a pH response of a Compound(24)-labeled goat-anti-human (GAH) Fab fragment: the solid line ispH=10, the diamond line is pH=8, the triangle line is pH=6, and thesquare line is pH=4.

FIG. 12 shows internalization of EGF-conjugated to Compound (24). Theleft panel shows cells pretreated with EGF and the right panel showscells treated with dye-conjugated EGF.

FIG. 13 shows internalization of Compound (33).

DETAILED DESCRIPTION

A family of rhodamine-based pH sensors (Smith, et. al; PCT PublicationNo. WO 2005/098437, herein incorporated by reference in its entirety)displays pH-dependency based on the ionization state of the Xsubstituent (see Scheme I below), namely a hydroxyl or thiol group, suchthat deprotonation of the —OH or —SH group to a negatively charged statequenches the fluorescence. It is only upon protonation of the negativelycharged —O⁻ or —S⁻ that the fluorescence is restored as illustrated inScheme 1:

However, we have unexpectedly found that alkoxy substitutions at thecorresponding X position are still capable of demonstrating a modulatedfluorescence in response to a change in pH. Thus, while not wishing tobe bound by a theory, we postulate that it is the protonation of thenitrogen at the 4 position on the aryl ring that modulates fluorescence.In any event, the present invention is predicated on the surprisingdiscovery that the hitherto indispensable hydroxy or thiol group X maybe dispensed with provided that a substituent nitrogen is retained.Advantageously, the addition of a dialkylamino group at the R³ positionresulted in a physiological pKa.

In addition, the pH-sensitive fluorescent dyes provided herein fluorescein the green portion of the UV/VIS spectrum and have different chemicalbehavior as compared to other pH-sensitive dyes. It was surprisinglydiscovered that: 1) the electron withdrawing power of the xanthenemoiety is significantly stronger in the pH-sensitive fluorescent dyesprovided herein, 2) the electron withdrawing power of the aniline moietymay be modulated by adding various electron donating groups to thebenzene ring, and 3) the addition of electron donating groups, such asdialkylamino groups at the R³ position and/or halogen at positions R²and/or R⁶, may be used to tune the pKa of the pH-sensitive fluorescentdyes to be at or near physiological pH. Furthermore, by altering theelectron donating groups at positions R₁-R⁶, the pKa of the pH-sensitivefluorescent dye may be modulated to suit a particular need.

Further, we have found that the dyes described by Smith et al. are notstable in solution, most likely as a result of aerobic oxidation (e.g.,oxidation by exposure to ambient air). In addition, strong electronwithdrawing properties of the reporter tetramethylrhodamine moiety ofthe dyes described in Smith et al (supra) significantly decrease the pKaof the indicator group at the X position of Scheme 1, thus shifting thesensors' working range towards acidic pH values.

In certain embodiments, therefore, the present invention providespH-sensitive fluorescent dyes having an aniline moiety (of which theamino group may be substituted or modified as disclosed herein) whereinthe benzene ring of the aniline moiety is free from hydroxy and thiolsubstituents ortho to the fluorophore or, in certain embodiments, freefrom hydroxy and thiol substituents at all positions. In particular,these pH-sensitive fluorescent dye compounds may have, in place of thehydroxy or thiol substituent required by Smith et al. (supra), a moietywherein the oxygen or sulfur of the hydroxy or thiol group has beenincorporated into an ether or thioether linkage, for example as part ofan alkoxy group or furan moiety, or their sulfur analogs. Viewedalternatively, the pH-sensitive fluorescent dye compounds providedherein which retain the oxygen or sulfur in etherified form, arepH-sensitive fluorescent dye compounds which provide increasedelectronic density of the molecule through strategic introduction ofelectron donating groups (EDG) to the benzene ring resulting in anelectron rich aniline moiety, thereby moving the pKa closer to aphysiological range (e.g., pH 6-8). Accordingly, the benzene ring may besubstituted one or more times (e.g., 1, 2, 3 or 4 times) by an electrondonating group, the electron donating groups being the same ordifferent. In certain embodiments, the pH-sensitive fluorescent dyecompounds provided herein have the etherified O or S replaced by anotherelectron donating group. Irrespective of whether the etherified O or Sis replaced by another EDG, supplementary electron donating groups maybe provided on the benzene ring to further modulate the pKa. In certainembodiments, the pH-sensitive fluorescent dye compounds provided hereinmay comprise two electron donating groups in total on the benzene ring,in particular two electron donating groups of the type having a lonepair of electrons available immediately next to the benzene ring (e.g.alkoxy or dialkylamino, optionally substituted as described herein).Additionally, modifications may be made to modulate the quantum yield ofthe pH-sensitive fluorescent dye compounds of the present disclosure.Thus, the pH-sensitive fluorescent dye compounds as disclosed hereinhave significant advantages over other PET-based dyes and advantageouslyprovide the benefit of having improved stability and/or a pKa in therange of physiological applications. In addition, the pKa of thepH-sensitive fluorescent dye compounds provided herein may be tuned toparticular pKa's depending on the electron donating group(s) used on thebenzene ring (e.g., on the aniline moiety). In addition, thepH-sensitive fluorescent dye compounds fluoresce in the green portion ofthe UV/VIS spectrum.

In certain embodiments, the pKa of the amino group on the aniline moietyis modulated by modifying the amino group into a more basic nitrogenfunctional group. This feature may usefully be adopted as an alternativeto replacing the omitted hydroxy or thiol group with another electrondonating group; alternatively, modification of the amino group into amore basic group may be combined with substitution of the benzene ringby at least one electron donating group other than a hydroxy or thiolgroup.

Also included herein are embodiments in which the pKa of the anilinemoiety is modulated by modifying the amino group at position R³ to—NR′R″, wherein R′ and R″, which may be the same or different, are eachindependently alkyl or substituted alkyl (e.g., a dialkylamino group) inorder to bring the pKa closer to the physiological range. In certainembodiments, the dialkylamino group is dimethylamino (e.g., —N(CH₃)₂).In certain embodiments, the dialkylamino group is diethylamino (e.g.,—N(CH₂CH₃)₂).

Particular features targeted by the compounds, compositions, methods andkits described herein include one or more of: (1) dissociation constantpKa within the physiological range; (2) greater stability (considered tobe towards oxidation); (3) flexible synthetic methods allowingintroduction of pKa-modulating substituents along with reactive groups;4) tuneability of the pKa; and 5) excitation and emission in the greenportion of the UV/VIS spectrum, which is the most common portion of theUV/VIS spectrum in terms of usage in biological systems and assays. Asdescribed previously herein, the pH-sensitive fluorescent dye compoundsof the present invention, have enhanced stability by dispensing with thepreviously indispensable hydroxy or thiol at position X of Scheme I, andthe hydroxy or thiol group is advantageously replaced by anotherelectron donating group at the same position, such as an alkoxy orthioalkyl, preferably an alkoxy. Additionally or alternatively, suchother electron donating groups may be substituted at other positions onthe benzene ring. In certain embodiments, such other electron donatinggroups include dialkylamino groups, wherein each alkyl group, which maybe the same or different, are each independently alkyl or substitutedalkyl. In certain embodiments, such other electron donating groupsinclude halogen, preferably, chloro and fluoro.

In order to achieve these goals a novel class of the pH-sensitivecompounds was designed, synthesized and tested in analytical andbiological applications. The structures of the preferred dye compoundsinclude structural formulae (I) and (II).

Substituents on an aromatic ring may either donate electrons to thearomatic ring or withdraw electrons from the aromatic ring as comparedto a hydrogen atom attached to the ring. Substituents may therefore beclassified as electron donating groups or electron withdrawing groups.

Many electron donating groups have lone pairs of electrons on the atomadjacent to the pi (π) system of the aromatic ring. Alkyl, aromatic andalkenyl groups are examples of electron donating groups. Electronwithdrawing groups are generally those where the atom adjacent to thearomatic pi system has a formal positive charge or a δ positive charge(for example, due to being connected to more electronegative atoms).Electron donating groups have an activating effect with respect tofurther substitution of the ring system and tend to direct furthersubstitution ortho/para, while electron withdrawing groups aredeactivating and tend to direct further substitution meta. The exceptionto this is halogen substituents, which, while overall electronwithdrawing and deactivating, tend to direct further substitutionortho/para due to resonance (lone pair) donation. Table 1 indicates therelative electron withdrawing and donating character of some commonsubstituents.

TABLE 1 Relative electron donating/withdrawing character of differentaromatic ring substituents, ranked from most electon donating to mostelectron withdrawing Character relative Activating/ Substituent to Hdeactivating Directing —O⁻ electron donating strongly activateortho/para —NR₂ electron donating strongly activate ortho/para —NH₂electron donating strongly activate ortho/para —OH electron donatingstrongly activate ortho/para —OR electron donating strongly activateortho/para —NHC(O)R electron donating moderately activate ortho/para—OC(O)R electron donating moderately activate ortho/para —R electrondonating weakly activate ortho/para —Ph electron donating weaklyactivate ortho/para —CH═CR₂ electron donating weakly activate ortho/para—H reference neutral ortho/para —X (X = halo) electron withdrawingweakly deactivate ortho/para —C(O)H electron withdrawing moderately de-meta activate —C(O)R electron withdrawing moderately de- meta activate—C(O)OR electron withdrawing moderately de- meta activate —C(O)OHelectron withdrawing moderately de- meta activate —CF₃ electronwithdrawing strongly deactivate meta —CN electron withdrawing stronglydeactivate meta —S(O)₂OH electron withdrawing strongly deactivate meta—N⁽⁺⁾H₃ electron withdrawing strongly deactivate meta —N⁽⁺⁾R₃ electronwithdrawing strongly deactivate meta —N⁽⁺⁾(O)O⁽⁻⁾ electron withdrawingstrongly deactivate meta

The symbol R in Table 1 in particular stands for alkyl, though it may besubstituted in any reasonable way which does not transform theelectronic effect of alkyl from donating to withdrawing or vice-versa.This specification further describes suitable electron donating groupsfor phenylic substitution of the aniline or aniline-like ring describedin the specification.

Definitions:

To more clearly and concisely describe and point out the subject matterof the present disclosure, the following definitions are provided forspecific terms, which are used in the following description and appendedclaims. Throughout the specification, exemplification of specific termsshould be considered as non-limiting examples.

Before describing the present teachings in detail, it is to beunderstood that the disclosure is not limited to specific compositionsor process steps, as such may vary. It should be noted that, as used inthis specification and the appended claims, the singular form “a”, “an”and “the” include plural references unless the context clearly dictatesotherwise. Thus, for example, reference to “a fluorescent pH sensitivedye” includes a plurality of dyes and reference to “a cell” includes aplurality of cells and the like. The phrase “and/or” denotes a shorthandway of indicating that the specific combination is contemplated incombination and separately, in the alternative. For illustrationpurposes, but not as a limitation, “X and/or Y” can mean “X” or “Y” or“X” and “Y”.

It will be appreciated that there is an implied “about” prior to thetemperatures, concentrations, times, etc. discussed in the presentdisclosure, such that slight and insubstantial deviations are within thescope of the present teachings herein. Also, the use of “comprise”,“comprises”, “comprising”, “contain”, “contains”, “containing”,“include”, “includes”, and “including” are not intended to be limiting.It is to be understood that both the foregoing general description anddetailed description are exemplary and explanatory only and are notrestrictive of the teachings.

Unless specifically noted in the above specification, embodiments in theabove specification that recite “comprising” various components are alsocontemplated as “consisting of” or “consisting essentially of” therecited components; embodiments in the specification that recite“consisting of” various components are also contemplated as “comprising”or “consisting essentially of” the recited components; and embodimentsin the specification that recite “consisting essentially of” variouscomponents are also contemplated as “consisting of” or “comprising” therecited components (this interchangeability does not apply to the use ofthese terms in the claims).

The term “or combinations thereof” as used herein refers to allpermutations and combinations of the listed terms preceding the term.For example, “A, B, C, or combinations thereof” is intended to includeat least one of: A, B, C, AB, AC, BC, or ABC, and if order is importantin a particular context, also BA, CA, CB, ACB, CBA, BCA, BAC, or CAB.Continuing with this example, expressly included are combinations thatcontain repeats of one or more item or term, such as BB, AAA, AAB, BBC,AAABCCCC, CBBAAA, CABABB, and so forth. The skilled artisan willunderstand that typically there is no limit on the number of items orterms in any combination, unless otherwise apparent from the context.

The section headings used herein are for organizational purposes onlyand are not to be construed as limiting the desired subject matter inany way. All literature cited in the specification, including but notlimited to, patents, patent applications, articles, books and treatisesare expressly incorporated by reference in their entirety for anypurpose. In the event that any of the incorporated literaturecontradicts any term defined in this specification, this specificationcontrols. While the present teachings are described in conjunction withvarious embodiments, it is not intended that the present teachings belimited to such embodiments. On the contrary, the present teachingsencompass various alternatives, modifications, and equivalents, as willbe appreciated by those of skill in the art.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this disclosure is related. The following terms aredefined for purposes of the teachings as described herein.

“Alkyl” refers to monovalent saturated aliphatic hydrocarbyl groupshaving from 1 to 10 carbon atoms and preferably 1 to 6 carbon atoms,e.g. 1, 2, 3, 4, 5 or 6 carbon atoms. This term includes, by way ofexample, linear and branched hydrocarbyl groups such as methyl (CH₃—),ethyl (CH₃CH₂—), n-propyl (CH₃CH₂CH₂—), isopropyl ((CH₃)₂CH—), n-butyl(CH₃CH₂CH₂CH₂—), isobutyl ((CH₃)₂CHCH₂—), sec-butyl ((CH₃)(CH₃CH₂)CH—),t-butyl ((CH₃)₃C—), n-pentyl (CH₃CH₂CH₂CH₂CH₂—), and neopentyl((CH₃)₃CCH₂—).

“Substituted alkyl” refers to an alkyl group having from 1 to 5,preferably 1 to 3, or more preferably 1 to 2 substituents selected fromthe group consisting of alkoxy, substituted alkoxy, acyl, acylamino,acyloxy, amino, substituted amino, aminocarbonyl, aminothiocarbonyl,aminocarbonylamino, aminothiocarbonylamino, aminocarbonyloxy,aminosulfonyl, aminosulfonyloxy, aminosulfonylamino, amidino, aryl,substituted aryl, aryloxy, substituted aryloxy, arylthio, substitutedarylthio, carboxyl, carboxylalkyl, carboxyl ester, (carboxylester)amino, (carboxyl ester)oxy, cyano, cycloalkyl, substitutedcycloalkyl, cycloalkyloxy, substituted cycloalkyloxy, cycloalkylthio,substituted cycloalkylthio, cycloalkenyl, substituted cycloalkenyl,cycloalkenyloxy, substituted cycloalkenyloxy, cycloalkenylthio,substituted cycloalkenylthio, guanidino, substituted guanidino, halo,hydroxy, heteroaryl, substituted heteroaryl, heteroaryloxy, substitutedheteroaryloxy, heteroarylthio, substituted heteroarylthio, heterocyclic,substituted heterocyclic, heterocyclyloxy, substituted heterocyclyloxy,heterocyclylthio, substituted heterocyclylthio, nitro, SO₃H, substitutedsulfonyl, sulfonyloxy, thioacyl, thiol, alkylthio, and substitutedalkylthio, wherein said substituents are defined herein. Particularsubstituted alkyl groups comprise a reactive group for direct orindirect linking to a carrier molecule or solid support, for example,but not limited to, alkyl substituted by carboxyl or a carboxyl ester(e.g. an activated ester such as an N-hydroxysuccinimide ester) andalkyl substituted by aminocarbonyl —CONHR where R is an organic moietyas defined below with reference to the term “aminocarbonyl”, e.g. aC₁-C₁₀ (e.g. C₁-C₆) alkyl terminally substituted by a reactive group(R_(x)) including, but not limited to, carboxyl, carboxylester,maleimide, succinimidyl ester (SE), sulfodichlorophenol (SDP) ester,sulfotetrafluorophenol (STP) ester, tetrafluorophenol (TFP) ester,acetoxymethoxy (AM) ester, nitrilotriacetic acid (NTA), aminodextran,and DIBO-amine.

“Alkoxy” refers to the group —O-alkyl wherein alkyl is defined herein.Alkoxy includes, by way of example, methoxy, ethoxy, n-propoxy,isopropoxy, n-butoxy, t-butoxy, sec-butoxy, and n-pentoxy.

“Substituted alkoxy” refers to the group —O-(substituted alkyl), whereinsubstituted alkyl is defined herein.

“Acyl” refers to the groups H—C(O)—, alkyl-C(O)—, substitutedalkyl-C(O)—, alkenyl-C(O)—, substituted alkenyl-C(O)—, alkynyl-C(O)—,substituted alkynyl-C(O)—, cycloalkyl-C(O)—, substitutedcycloalkyl-C(O)—, cycloalkenyl-C(O)—, substituted cycloalkenyl-C(O)—,aryl-C(O)—, substituted aryl-C(O)—, heteroaryl-C(O)—, substitutedheteroaryl-C(O)—, heterocyclic-C(O)—, and substitutedheterocyclic-C(O)—, wherein alkyl, substituted alkyl, alkenyl,substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl,substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, heterocyclic andsubstituted heterocyclic are as defined herein. Acyl includes the“acetyl” group CH₃C(O)—.

“Acylamino” refers to the groups —NRC(O)alkyl, —NRC(O)substituted alkyl,—NRC(O)cycloalkyl, —NRC(O)substituted cycloalkyl, —NRC(O)cycloalkenyl,—NRC(O)substituted cycloalkenyl, —NRC(O)alkenyl, —NRC(O)substitutedalkenyl, —NRC(O)alkynyl, —NRC(O)substituted alkynyl, —NRC(O)aryl,—NRC(O)substituted aryl, —NRC(O)heteroaryl, —NRC(O)substitutedheteroaryl, —NRC(O)heterocyclic, and —NRC(O)substituted heterocyclic,wherein R is hydrogen or alkyl and wherein alkyl, substituted alkyl,alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl,substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, heterocyclic andsubstituted heterocyclic are as defined herein.

“Acyloxy” refers to the groups alkyl-C(O)O—, substituted alkyl-C(O)O—,alkenyl-C(O)O—, substituted alkenyl-C(O)O—, alkynyl-C(O)O—, substitutedalkynyl-C(O)O—, aryl-C(O)O—, substituted aryl-C(O)O—, cycloalkyl-C(O)O—,substituted cycloalkyl-C(O)O—, cycloalkenyl-C(O)O—, substitutedcycloalkenyl-C(O)O—, heteroaryl-C(O)O—, substituted heteroaryl-C(O)O—,heterocyclic-C(O)O—, and substituted heterocyclic-C(O)O—, wherein alkyl,substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substitutedalkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substitutedcycloalkenyl, aryl, substituted aryl, heteroaryl, substitutedheteroaryl, heterocyclic, and substituted heterocyclic are as definedherein.

Amino” refers to the group —NH₂.

“Substituted amino” refers to the group —NR′R″ where R′ and R″ areindependently selected from the group consisting of hydrogen, alkyl,substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substitutedalkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl,cycloalkenyl, substituted cycloalkenyl, heteroaryl, substitutedheteroaryl, heterocyclic, substituted heterocyclic, —SO₂-alkyl,—SO₂-substituted alkyl, —SO₂-alkenyl, —SO₂-substituted alkenyl,—SO₂-cycloalkyl, —SO₂-substituted cylcoalkyl, —SO₂-cycloalkenyl,—SO₂-substituted cylcoalkenyl,—SO₂-aryl, —SO₂-substituted aryl,—SO₂-heteroaryl, —SO₂-substituted heteroaryl, —SO₂-heterocyclic, and—SO₂-substituted heterocyclic and wherein R′ and R″ are optionallyjoined, together with the nitrogen bound thereto to form a heterocyclicor substituted heterocyclic group, provided that R′ and R″ are both nothydrogen, and wherein alkyl, substituted alkyl, alkenyl, substitutedalkenyl, alkynyl, substituted alkynyl, cycloalkyl, substitutedcycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl, substitutedaryl, heteroaryl, substituted heteroaryl, heterocyclic, and substitutedheterocyclic are as defined herein. When R′ is hydrogen and R″ is alkyl,the substituted amino group is sometimes referred to herein asalkylamino. When R′ and R″ are alkyl, the substituted amino group issometimes referred to herein as dialkylamino. When referring to amonosubstituted amino, it is meant that either R′ or R″ is hydrogen butnot both. When referring to a disubstituted amino, it is meant thatneither R′ nor R″ are hydrogen.

“Aminocarbonyl” refers to the group —C(O)NR′R″ where R′ and R″ areindependently selected from the group consisting of hydrogen, alkyl,substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substitutedalkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl,cycloalkenyl, substituted cycloalkenyl, heteroaryl, substitutedheteroaryl, heterocyclic, and substituted heterocyclic, and where R′ andR″ are optionally joined together with the nitrogen bound thereto toform a heterocyclic or substituted heterocyclic group, and whereinalkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,substituted alkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl,substituted cycloalkenyl, aryl, substituted aryl, heteroaryl,substituted heteroaryl, heterocyclic and substituted heterocyclic are asdefined herein.

“Aminothiocarbonyl” refers to the group —C(S)NR′R″ where R′ and R″ areindependently selected from the group consisting of hydrogen, alkyl,substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substitutedalkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl,cycloalkenyl, substituted cycloalkenyl, heteroaryl, substitutedheteroaryl, heterocyclic, and substituted heterocyclic, and where R′ andR″ are optionally joined together with the nitrogen bound thereto toform a heterocyclic or substituted heterocyclic group, and whereinalkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,substituted alkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl,substituted cycloalkenyl, aryl, substituted aryl, heteroaryl,substituted heteroaryl, heterocyclic and substituted heterocyclic are asdefined herein.

“Aminocarbonylamino” refers to the group —NRC(O)NR′R″ where R ishydrogen or alkyl and R′ and R″ are independently selected from thegroup consisting of hydrogen, alkyl, substituted alkyl, alkenyl,substituted alkenyl, alkynyl, substituted alkynyl, aryl, substitutedaryl, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substitutedcycloalkenyl, heteroaryl, substituted heteroaryl, heterocyclic, andsubstituted heterocyclic, and where R′ and R″ are optionally joinedtogether with the nitrogen bound thereto to form a heterocyclic orsubstituted heterocyclic group, and wherein alkyl, substituted alkyl,alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl,substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, heterocyclic andsubstituted heterocyclic are as defined herein.

“Aminothiocarbonylamino” refers to the group —NRC(S)NR′R″ where R ishydrogen or alkyl and R′ and R″ are independently selected from thegroup consisting of hydrogen, alkyl, substituted alkyl, alkenyl,substituted alkenyl, alkynyl, substituted alkynyl, aryl, substitutedaryl, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substitutedcycloalkenyl, heteroaryl, substituted heteroaryl, heterocyclic, andsubstituted heterocyclic, and where R′ and R″ are optionally joinedtogether with the nitrogen bound thereto to form a heterocyclic orsubstituted heterocyclic group, and wherein alkyl, substituted alkyl,alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl,substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, heterocyclic andsubstituted heterocyclic are as defined herein.

“Aminocarbonyloxy” refers to the group —O—C(O)NR′R″ where R′ and R″ areindependently selected from the group consisting of hydrogen, alkyl,substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substitutedalkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl,cycloalkenyl, substituted cycloalkenyl, heteroaryl, substitutedheteroaryl, heterocyclic, and substituted heterocyclic and where R′ andR″ are optionally joined together with the nitrogen bound thereto toform a heterocyclic or substituted heterocyclic group, and whereinalkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,substituted alkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl,substituted cycloalkenyl, aryl, substituted aryl, heteroaryl,substituted heteroaryl, heterocyclic and substituted heterocyclic are asdefined herein.

“Aminosulfonyl” refers to the group —SO₂NR′R″ where R′ and R″ areindependently selected from the group consisting of hydrogen, alkyl,substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substitutedalkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl,cycloalkenyl, substituted cycloalkenyl, heteroaryl, substitutedheteroaryl, heterocyclic, and substituted heterocyclic, and where R′ andR″ are optionally joined together with the nitrogen bound thereto toform a heterocyclic or substituted heterocyclic group, and whereinalkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,substituted alkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl,substituted cycloalkenyl, aryl, substituted aryl, heteroaryl,substituted heteroaryl, heterocyclic and substituted heterocyclic are asdefined herein.

“Aminosulfonyloxy” refers to the group —O—SO₂NR′R″ where R′ and R″ areindependently selected from the group consisting of hydrogen, alkyl,substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substitutedalkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl,cycloalkenyl, substituted cycloalkenyl, heteroaryl, substitutedheteroaryl, heterocyclic, and substituted heterocyclic, and where R′ andR″ are optionally joined together with the nitrogen bound thereto toform a heterocyclic or substituted heterocyclic group, and whereinalkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,substituted alkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl,substituted cycloalkenyl, aryl, substituted aryl, heteroaryl,substituted heteroaryl, heterocyclic and substituted heterocyclic are asdefined herein.

“Aminosulfonylamino” refers to the group —NR—SO₂NR′R″ where R ishydrogen or alkyl and R′ and R″ are independently selected from thegroup consisting of hydrogen, alkyl, substituted alkyl, alkenyl,substituted alkenyl, alkynyl, substituted alkynyl, aryl, substitutedaryl, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substitutedcycloalkyenyl, heteroaryl, substituted heteroaryl, heterocyclic, andsubstituted heterocyclic, and where R′ and R″ are optionally joinedtogether with the nitrogen bound thereto to form a heterocyclic orsubstituted heterocyclic group, and wherein alkyl, substituted alkyl,alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl,substituted cycloalkyl, cycloalkenyl, substituted cycloalkyenyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, heterocyclic andsubstituted heterocyclic are as defined herein.

“Amidino” refers to the group —C(═NR′″)R′R″ where R′, R″, and R′″ areindependently selected from the group consisting of hydrogen, alkyl,substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substitutedalkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl,cycloalkenyl, substituted cycloalkenyl, heteroaryl, substitutedheteroaryl, heterocyclic, and substituted heterocyclic, and where R′ andR″ are optionally joined together with the nitrogen bound thereto toform a heterocyclic or substituted heterocyclic group, and whereinalkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,substituted alkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl,substituted cycloalkenyl, aryl, substituted aryl, heteroaryl,substituted heteroaryl, heterocyclic and substituted heterocyclic are asdefined herein.

“Aniline” refers to C₆H₅NH₂, and consists of a phenyl ring attached toan amino group. As used herein, the amino group is para to afluorophore, as is illustrated as follows:

wherein X is a fluorophore, preferably a xanthene derivative, mostpreferably a rhodamine or rhodol.

“Aryl” or “Ar” refers to a monovalent aromatic carbocyclic group of from6 to 14 carbon atoms having a single ring (e.g., phenyl) or multiplecondensed rings (e.g., naphthyl or anthryl) which condensed rings may ormay not be aromatic (e.g., 2-benzoxazolinone,2H-1,4-benzoxazin-3(4H)-one-7-yl, and the like) provided that the pointof attachment is at an aromatic carbon atom. Preferred aryl groupsinclude phenyl and naphthyl.

“Substituted aryl” refers to aryl groups which are substituted with 1 to5, preferably 1 to 3, or more preferably 1 to 2 substituents selectedfrom the group consisting of alkyl, substituted alkyl, alkenyl,substituted alkenyl, alkynyl, substituted alkynyl, alkoxy, substitutedalkoxy, acyl, acylamino, acyloxy, amino, substituted amino,aminocarbonyl, aminothiocarbonyl, aminocarbonylamino,aminothiocarbonylamino, aminocarbonyloxy, aminosulfonyl,aminosulfonyloxy, aminosulfonylamino, amidino, aryl, substituted aryl,aryloxy, substituted aryloxy, arylthio, substituted arylthio, carboxyl,carboxyl ester, (carboxyl ester)amino, (carboxyl ester)oxy, cyano,cycloalkyl, substituted cycloalkyl, cycloalkyloxy, substitutedcycloalkyloxy, cycloalkylthio, substituted cycloalkylthio, cycloalkenyl,substituted cycloalkenyl, cycloalkenyloxy, substituted cycloalkenyloxy,cycloalkenylthio, substituted cycloalkenylthio, guanidino, substitutedguanidino, halo, hydroxy, heteroaryl, substituted heteroaryl,heteroaryloxy, substituted heteroaryloxy, heteroarylthio, substitutedheteroarylthio, heterocyclic, substituted heterocyclic, heterocyclyloxy,substituted heterocyclyloxy, heterocyclylthio, substitutedheterocyclylthio, nitro, SO₃H, substituted sulfonyl, sulfonyloxy,thioacyl, thiol, alkylthio, and substituted alkylthio, wherein saidsubstituents are defined herein.

“Aryloxy” refers to the group —O-aryl, where aryl is as defined herein,that includes, by way of example, phenoxy and naphthoxy.

“Substituted aryloxy” refers to the group —O-(substituted aryl), wheresubstituted aryl is as defined herein.

“Arylthio” refers to the group —S-aryl, where aryl is as defined herein.

“Substituted arylthio” refers to the group —S-(substituted aryl), wheresubstituted aryl is as defined herein.

“Alkenyl” refers to alkenyl groups having from 2 to 6 carbon atoms andpreferably 2 to 4 carbon atoms and having at least 1 and preferably from1 to 2 sites of alkenyl unsaturation. Such groups are exemplified, forexample, by vinyl, allyl, but-3-en-1-yl, and propenyl.

“Substituted alkenyl” refers to alkenyl groups having from 1 to 3substituents, and preferably 1 to 2 substituents, selected from thegroup consisting of alkoxy, substituted alkoxy, acyl, acylamino,acyloxy, amino, substituted amino, aminocarbonyl, aminothiocarbonyl,aminocarbonylamino, aminothiocarbonylamino, aminocarbonyloxy,aminosulfonyl, aminosulfonyloxy, aminosulfonylamino, amidino, aryl,substituted aryl, aryloxy, substituted aryloxy, arylthio, substitutedarylthio, carboxyl, carboxyl ester, (carboxyl ester)amino, (carboxylester)oxy, cyano, cycloalkyl, substituted cycloalkyl, cycloalkyloxy,substituted cycloalkyloxy, cycloalkylthio, substituted cycloalkylthio,cycloalkenyl, substituted cycloalkenyl, cycloalkenyloxy, substitutedcycloalkenyloxy, cycloalkenylthio, substituted cycloalkenylthio,guanidino, substituted guanidino, halo, hydroxy, heteroaryl, substitutedheteroaryl, heteroaryloxy, substituted heteroaryloxy, heteroarylthio,substituted heteroarylthio, heterocyclic, substituted heterocyclic,heterocyclyloxy, substituted heterocyclyloxy, heterocyclylthio,substituted heterocyclylthio, nitro, SO₃H, substituted sulfonyl,sulfonyloxy, thioacyl, thiol, alkylthio, and substituted alkylthio,wherein said substituents are defined herein and with the proviso thatany hydroxy substitution is not attached to a vinyl (unsaturated) carbonatom.

“Alkynyl” refers to alkynyl groups having from 2 to 6 carbon atoms andpreferably 2 to 3 carbon atoms and having at least 1 and preferably from1 to 2 sites of alkynyl unsaturation.

“Substituted alkynyl” refers to alkynyl groups having from 1 to 3substituents, and preferably 1 to 2 substituents, selected from thegroup consisting of alkoxy, substituted alkoxy, acyl, acylamino,acyloxy, amino, substituted amino, aminocarbonyl, aminothiocarbonyl,aminocarbonylamino, aminothiocarbonylamino, aminocarbonyloxy,aminosulfonyl, aminosulfonyloxy, aminosulfonylamino, amidino, aryl,substituted aryl, aryloxy, substituted aryloxy, arylthio, substitutedarylthio, carboxyl, carboxyl ester, (carboxyl ester)amino, (carboxylester)oxy, cyano, cycloalkyl, substituted cycloalkyl, cycloalkyloxy,substituted cycloalkyloxy, cycloalkylthio, substituted cycloalkylthio,cycloalkenyl, substituted cycloalkenyl, cycloalkenyloxy, substitutedcycloalkenyloxy, cycloalkenylthio, substituted cycloalkenylthio,guanidino, substituted guanidino, halo, hydroxy, heteroaryl, substitutedheteroaryl, heteroaryloxy, substituted heteroaryloxy, heteroarylthio,substituted heteroarylthio, heterocyclic, substituted heterocyclic,heterocyclyloxy, substituted heterocyclyloxy, heterocyclylthio,substituted heterocyclylthio, nitro, SO₃H, substituted sulfonyl,sulfonyloxy, thioacyl, thiol, alkylthio, and substituted alkylthio,wherein said substituents are defined herein and with the proviso thatany hydroxy substitution is not attached to an acetylenic carbon atom.

“Carbonyl” refers to the divalent group —C(O)— which is equivalent to−C(═O)—.

“Carboxyl” or “carboxy” refers to —COOH or salts thereof.

“Carboxyl alkyl” or “carboxyalkyl” refers to the group —(CH₂)_(n)COOH,where n is 1-6.

“Carboxyl ester” or “carboxy ester” refers to the groups —C(O)O-alkyl,—C(O)O-substituted alkyl, —C(O)O-alkenyl, —C(O)O-substituted alkenyl,—C(O)O-alkynyl, —C(O)O-substituted alkynyl, —C(O)O-aryl,—C(O)O-substituted aryl, —C(O)O-cycloalkyl, —(O)O-substitutedcycloalkyl, —(O)O-cycloalkenyl, —(O)O-substituted cycloalkenyl,—(O)O-heteroaryl, —(O)O-substituted heteroaryl, —(O)O-heterocyclic, and—(O)O-substituted heterocyclic, wherein alkyl, substituted alkyl,alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl,substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, heterocyclic, andsubstituted heterocyclic are as defined herein.

“(Carboxyl ester)amino” refers to the group —NR—C(O)O-alkyl, substituted—NR—C(O)O-alkyl, —NR—C(O)O-alkenyl, —NR—C(O)O-substituted alkenyl,—NR—C(O)O-alkynyl, —NR—C(O)O-substituted alkynyl, —NR—C(O)O-aryl,—NR—C(O)O-substituted aryl, —NR—C(O)O-cycloalkyl, —NR—C(O)O-substitutedcycloalkyl, —NR—C(O)O-cycloalkenyl, —NR—C(O)O-substituted cycloalkenyl,—NR—C(O)O-heteroaryl, —NR—C(O)O-substituted heteroaryl,—NR—C(O)O-heterocyclic, and —NR—C(O)O-substituted heterocyclic, whereinR is alkyl or hydrogen, and wherein alkyl, substituted alkyl, alkenyl,substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl,substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, heterocyclic, andsubstituted heterocyclic are as defined herein.

“(Carboxyl ester)oxy” refers to the group —O—(O)O-alkyl, substituted—O—(O)O-alkyl, —O—C(O)O-alkenyl, —O—C(O)O-substituted alkenyl,—O—C(O)O-alkynyl, —O—C(O)O-substituted alkynyl, —O—(O)O-aryl,—O—C(O)O-substituted aryl, —O—C(O)O-cycloalkyl, —O—C(O)O-substitutedcycloalkyl, —O—C(O)O-cycloalkenyl, —O—C(O)O-substituted cycloalkenyl,—O—C(O)O-heteroaryl, —O—C(O)O-substituted heteroaryl,—O—C(O)O-heterocyclic, and —O—C(O)O-substituted heterocyclic, whereinalkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,substituted alkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl,substituted cycloalkenyl, aryl, substituted aryl, heteroaryl,substituted heteroaryl, heterocyclic, and substituted heterocyclic areas defined herein.

“Cyano” refers to the group —CN.

“Cycloalkyl” refers to cyclic alkyl groups of from 3 to 10 carbon atomshaving single or multiple cyclic rings including fused, bridged, andspiro ring systems. Examples of suitable cycloalkyl groups include, forinstance, adamantyl, cyclopropyl, cyclobutyl, cyclopentyl, andcyclooctyl.

“Cycloalkenyl” refers to non-aromatic cyclic alkyl groups of from 3 to10 carbon atoms having single or multiple cyclic rings and having atleast one >C=C<ring unsaturation and preferably from 1 to 2 sitesof >C═C< ring unsaturation.

“Substituted cycloalkyl” and “substituted cycloalkenyl” refers to acycloalkyl or cycloalkenyl group having from 1 to 5 or preferably 1 to 3substituents selected from the group consisting of oxo, thione, alkyl,substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substitutedalkynyl, alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino,substituted amino, aminocarbonyl, aminothiocarbonyl, aminocarbonylamino,aminothiocarbonylamino, aminocarbonyloxy, aminosulfonyl,aminosulfonyloxy, aminosulfonylamino, amidino, aryl, substituted aryl,aryloxy, substituted aryloxy, arylthio, substituted arylthio, carboxyl,carboxyl ester, (carboxyl ester)amino, (carboxyl ester)oxy, cyano,cycloalkyl, substituted cycloalkyl, cycloalkyloxy, substitutedcycloalkyloxy, cycloalkylthio, substituted cycloalkylthio, cycloalkenyl,substituted cycloalkenyl, cycloalkenyloxy, substituted cycloalkenyloxy,cycloalkenylthio, substituted cycloalkenylthio, guanidino, substitutedguanidino, halo, hydroxy, heteroaryl, substituted heteroaryl,heteroaryloxy, substituted heteroaryloxy, heteroarylthio, substitutedheteroarylthio, heterocyclic, substituted heterocyclic, heterocyclyloxy,substituted heterocyclyloxy, heterocyclylthio, substitutedheterocyclylthio, nitro, SO₃H, substituted sulfonyl, sulfonyloxy,thioacyl, thiol, alkylthio, and substituted alkylthio, wherein saidsubstituents are defined herein.

“Cycloalkyloxy” refers to —O-cycloalkyl.

“Substituted cycloalkyloxy” refers to —O-(substituted cycloalkyl).

“Cycloalkylthio” refers to —S-cycloalkyl.

“Substituted cycloalkylthio” refers to —S-(substituted cycloalkyl).

“Cycloalkenyloxy” refers to —O-cycloalkenyl.

“Substituted cycloalkenyloxy” refers to —O-(substituted cycloalkenyl).

“Cycloalkenylthio” refers to —S-cycloalkenyl.

“Substituted cycloalkenylthio” refers to —S-(substituted cycloalkenyl).

“Guanidino” refers to the group —NHC(═NH)NH₂.

“Substituted guanidino” refers to —NR¹³C(═NR¹³)N(R¹³)₂ where each R¹³ isindependently selected from the group consisting of hydrogen, alkyl,substituted alkyl, aryl, substituted aryl, heteroaryl, substitutedheteroaryl, heterocyclic, and substituted heterocyclic and two R¹³groups attached to a common guanidino nitrogen atom are optionallyjoined together with the nitrogen bound thereto to form a heterocyclicor substituted heterocyclic group, provided that at least one R¹³ is nothydrogen, and wherein said substituents are as defined herein.

“H” indicates hydrogen.

“Halo” or “halogen” refers to fluoro, chloro, bromo and iodo.

“Hydroxy” or “hydroxyl” refers to the group —OH.

“Heteroaryl” refers to an aromatic group of from 1 to 10 carbon atomsand 1 to 4 heteroatoms selected from the group consisting of oxygen,nitrogen and sulfur within the ring. Such heteroaryl groups can have asingle ring (e.g., pyridinyl or furyl) or multiple condensed rings(e.g., indolizinyl or benzothienyl) wherein the condensed rings may ormay not be aromatic and/or contain a heteroatom provided that the pointof attachment is through an atom of the aromatic heteroaryl group. Inone embodiment, the nitrogen and/or the sulfur ring atom(s) of theheteroaryl group are optionally oxidized to provide for the N-oxide(N→O), sulfinyl, or sulfonyl moieties. Preferred heteroaryls includepyridinyl, pyrrolyl, indolyl, thiophenyl, and furanyl.

“Substituted heteroaryl” refers to heteroaryl groups that aresubstituted with from 1 to 5, preferably 1 to 3, or more preferably 1 to2 substituents selected from the group consisting of the same group ofsubstituents defined for substituted aryl.

“Heteroaryloxy” refers to —O-heteroaryl.

“Substituted heteroaryloxy” refers to the group —O-(substitutedheteroaryl).

“Heteroarylthio” refers to the group —S-heteroaryl.

“Substituted heteroarylthio” refers to the group —S-(substitutedheteroaryl).

“Heterocycle” or “heterocyclic” or “heterocycloalkyl” or “heterocyclyl”refers to a saturated or unsaturated group having a single ring ormultiple condensed rings, including fused bridged and spiro ringsystems, from 1 to 10 carbon atoms and from 1 to 4 hetero atoms selectedfrom the group consisting of nitrogen, sulfur or oxygen within the ringwherein, in fused ring systems, one or more the rings can be cycloalkyl,aryl or heteroaryl provided that the point of attachment is through thenon-aromatic ring. In one embodiment, the nitrogen and/or sulfur atom(s)of the heterocyclic group are optionally oxidized to provide for theN-oxide, sulfinyl, sulfonyl moieties.

“Substituted heterocyclic” or “substituted heterocycloalkyl” or“substituted heterocyclyl” refers to heterocyclyl groups that aresubstituted with from 1 to 5, or preferably 1 to 3 of the samesubstituents as defined for substituted cycloalkyl.

“Heterocyclyloxy” refers to the group —O-heterocyclyl.

“Substituted heterocyclyloxy” refers to the group —O-(substitutedheterocyclyl).

“Heterocyclylthio” refers to the group —S-heterocyclyl.

“Substituted heterocyclylthio” refers to the group —S-(substitutedheterocyclyl).

Examples of heterocycle and heteroaryls include, but are not limited to,azetidine, pyrrole, imidazole, pyrazole, pyridine, pyrazine, pyrimidine,pyridazine, indolizine, isoindole, indole, dihydroindole, indazole,purine, quinolizine, isoquinoline, quinoline, phthalazine,naphthylpyridine, quinoxaline, quinazoline, cinnoline, pteridine,carbazole, carboline, phenanthridine, acridine, phenanthroline,isothiazole, phenazine, isoxazole, phenoxazine, phenothiazine,imidazolidine, imidazoline, piperidine, piperazine, indoline,phthalimide, 1,2,3,4-tetrahydroisoquinoline,4,5,6,7-tetrahydrobenzo[b]thiophene, thiazole, thiazolidine, thiophene,benzo[b]thiophene, morpholinyl, thiomorpholinyl (also referred to asthiamorpholinyl), 1,1-dioxothiomorpholinyl, piperidinyl, pyrrolidine,and tetrahydrofuranyl.

“Hydrazinyl” refers to the group —NHNH₂— or ═NNH—.

“Substituted hydrazinyl” refers to a hydrazinyl group, wherein anon-hydrogen atom, such as an alkyl group, is appended to one or both ofthe hydrazinyl amine groups. An example of substituted hydrazinyl is—N(alkyl)—NH₂ or ═N⁺(alkyl)-NH₂.

“Nitro” refers to the group —NO₂.

“Oxo” refers to the atom (═O) or (—O).

“Spirocyclyl” refers to divalent saturated cyclic group from 3 to 10carbon atoms having a cycloalkyl or heterocyclyl ring with a spiro union(the union formed by a single atom which is the only common member ofthe rings) as exemplified by the following structure:

“Sulfonyl” refers to the divalent group —S(O)₂—.

“Substituted sulfonyl” refers to the group —SO₂-alkyl, —SO₂-substitutedalkyl, —SO₂-alkenyl, —SO₂-substituted alkenyl, —SO₂-cycloalkyl,—SO₂-substituted cylcoalkyl, —SO₂-cycloalkenyl, —SO₂-substitutedcylcoalkenyl, —SO₂-aryl, —SO₂-substituted aryl, —SO₂-heteroaryl,—SO₂-substituted heteroaryl, —SO₂-heterocyclic, —SO₂-substitutedheterocyclic, wherein alkyl, substituted alkyl, alkenyl, substitutedalkenyl, alkynyl, substituted alkynyl, cycloalkyl, substitutedcycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl, substitutedaryl, heteroaryl, substituted heteroaryl, heterocyclic and substitutedheterocyclic are as defined herein. Substituted sulfonyl includes groupssuch as methyl-SO₂—, phenyl—SO₂—, and 4-methylphenyl-SO₂—.

“Sulfonyloxy” refers to the group —OSO₂-alkyl, —OSO₂-substituted alkyl,—OSO₂-alkenyl, —OSO₂-substituted alkenyl, —OSO₂-cycloalkyl,—OSO₂-substituted cylcoalkyl, —OSO₂-cycloalkenyl, —OSO₂-substitutedcylcoalkenyl, —OSO₂-aryl, —OSO₂-substituted aryl, —OSO₂-heteroaryl,—OSO₂-substituted heteroaryl, —OSO₂-heterocyclic, —OSO₂-substitutedheterocyclic, wherein alkyl, substituted alkyl, alkenyl, substitutedalkenyl, alkynyl, substituted alkynyl, cycloalkyl, substitutedcycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl, substitutedaryl, heteroaryl, substituted heteroaryl, heterocyclic and substitutedheterocyclic are as defined herein.

“Thioacyl” refers to the groups H—C(S)—, alkyl-C(S)—, substitutedalkyl-C(S)—, alkenyl-C(S)—, substituted alkenyl-C(S)—, alkynyl-C(S)—,substituted alkynyl-C(S)—, cycloalkyl-C(S)—, substitutedcycloalkyl-C(S)—, cycloalkenyl-C(S)—, substituted cycloalkenyl-C(S)—,aryl-C(S)—, substituted aryl-C(S)—, heteroaryl-C(S)—, substitutedheteroaryl-C(S)—, heterocyclic-C(S)—, and substitutedheterocyclic-C(S)—, wherein alkyl, substituted alkyl, alkenyl,substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl,substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, heterocyclic andsubstituted heterocyclic are as defined herein.

“Thiol” refers to the group —SH.

“Thiocarbonyl” refers to the divalent group —C(S)— which is equivalentto —C(═S)—.

“Thione” refers to the atom (═S).

“Alkylthio” refers to the group —S-alkyl wherein alkyl is as definedherein.

“Substituted alkylthio” refers to the group —S-(substituted alkyl),wherein substituted alkyl is as defined herein.

A dashed line projecting from a substituent, such as:

indicates the point of attachment to the base molecule. For a fusedring, dashed lines indicate portions of the base molecule where thefused ring is attached, such as:

wherein the full molecule could have the structure:

Unless indicated otherwise, the nomenclature of substituents that arenot explicitly defined herein are arrived at by naming the terminalportion of the functionality followed by the adjacent functionalitytoward the point of attachment. For example, the substituent“arylalkyloxycarbonyl” refers to the group (aryl)-(alkyl)-O—C(O)—.

It is understood that in all substituted groups defined above, polymersarrived at by defining substituents with further substituents tothemselves (e.g., substituted aryl having a substituted aryl group as asubstituent which is itself substituted with a substituted aryl group,which is further substituted by a substituted aryl group etc.) are notintended for inclusion herein. In such cases, the maximum number of suchsubstitutions is three. For example, serial substitutions of substitutedaryl groups with two other substituted aryl groups are limitedto—substituted aryl-(substituted aryl)-substituted aryl.

Similarly, it is understood that the above definitions are not intendedto include impermissible substitution patterns (e.g., methyl substitutedwith 5 fluoro groups). Such impermissible substitution patterns are wellknown to the skilled artisan.

The pH-sensitive fluorescent dye compounds disclosed herein may exist inunsolvated forms as well as solvated forms, including hydrated forms.These compounds may exist in multiple crystalline or amorphous forms. Ingeneral, all physical forms are equivalent for the uses described hereinand are intended to be within the scope of the present disclosure. Thedye compounds disclosed herein may possess asymmetric carbon atoms(i.e., chiral centers) or double bonds; the racemates, diastereomers,geometric isomers and individual isomers of the compounds describedherein are within the scope of the present disclosure. The dye compoundsdescribed herein may be prepared as a single isomer or as a mixture ofisomers.

Where substituent groups are specified by their conventional chemicalformulae and are written from left to right, they equally encompass thechemically identical substituents, which would result from writing thestructure from right to left, e.g., —CH₂O— is intended to also recite—OCH₂—.

It will be understood that the chemical structures that are used todefine the dye compounds disclosed herein are each representations ofone of the possible resonance structures by which each given structurecan be represented. Further, it will be understood that by definition,resonance structures are merely a graphical representation used by thoseof skill in the art to represent electron delocalization, and that thepresent disclosure is not limited in any way by showing one particularresonance structure for any given structure.

Where a disclosed compound includes a conjugated ring system, resonancestabilization may permit a formal electronic charge to be distributedover the entire molecule. While a particular charge may be depicted aslocalized on a particular ring system, or a particular heteroatom, it iscommonly understood that a comparable resonance structure can be drawnin which the charge may be formally localized on an alternative portionof the compound.

The term “carrier molecule” as used herein, refers to a biological or anon-biological component that is or becomes covalently bonded to apH-sensitive fluorescent dye compound disclosed herein. Such componentsinclude, but are not limited to, an amino acid, a peptide, a protein, apolysaccharide, a nucleoside, a nucleotide, an oligonucleotide, anucleic acid, a hapten, a psoralen, a drug, a hormone, a lipid, a lipidassembly, a synthetic polymer, a polymeric microparticle, a biologicalcell, a virus and combinations thereof. Included is one embodiment inwhich carrier molecules comprise an organic moiety having at least 4plural valent atoms and often more than 10 plural valent atoms (i.e.,atoms other than hydrogen and halo), e.g. at least 15 such atoms, as inthe case of moieties having at least 20 such atoms.

The term “conjugated substance” or “S_(c)” refers to a carrier moleculeor solid support.

The term “detectable response” as used herein refers to an occurrence ofor a change in, a signal that is directly or indirectly detectableeither by observation or by instrumentation. Typically, the detectableresponse is an optical response resulting in a change in the wavelengthdistribution patterns or intensity of absorbance or fluorescence or achange in light scatter, fluorescence lifetime, fluorescencepolarization, or a combination of the above parameters.

The term “dye” as used herein refers to a compound that emits light toproduce an observable detectable signal.

The term “electron donating group” or “EDG” refers to a substituent withlone electron pairs that is adjacent to an aromatic ring, such asphenyl, and increases electron density on the ring through a resonancedonating effect. Electron donating groups of the present disclosureinclude, for example, alkoxy, substituted alkoxy, amino, substitutedamino, alkylthio, acylamino, (carboxyl ester)oxy, and halogen. Alkoxy isa particular EDG. Substituted alkoxy is another particular EDG. Also tobe mentioned is dialkylamino. A further example is dialkylamino having asubstituted alkyl group. Preferred EDGs are —OCH₃, —NH₂, —NHCH₃,—N(CH₃)₂, and —N(CH₂CH₃)₂, particularly —OCH₃, —NH₂, —NHCH₃, —N(CH₃)₂and —N(CH₂CH₃)₂. Also to be mentioned are alkoxy, alkythio anddialkylamino, in any of those instances having an alkyl substituent inwhich the alkyl part is substituted by a moiety -L-R_(x), -L-S_(c), or-L_(R)-S_(c). The specification also discloses specific compounds orcompound classes which include other EDGs than those with a lone pair ofelectrons adjacent an aromatic ring.

“Fluorescent pH-sensitive dye,” “pH-sensitive fluorescent dye,” and“fluorescent pH sensor dye” are equivalent and are used interchangeablyto refer to a compound whose fluorescent spectrum or intensity isaffected by pH.

The term “fluorophore” or “fluorogenic” as used herein refers to acomposition that is inherently fluorescent or demonstrates a change influorescence upon protonation, or binding to a biological compound ormetal ion, or metabolism by an enzyme. Preferred fluorophores of thepresent disclosure include fluorescent dyes having a high quantum yieldin aqueous media. Exemplary fluorophores include xanthene derivatives,preferably rhodamines and rhodols. The fluorophores disclosed herein maybe substituted to alter the solubility, spectral properties or physicalproperties of the fluorophore.

The term “linker” or “L”, as used herein, refers to a single covalentbond or a moiety comprising series of stable covalent bonds, the moietyoften incorporating 1-40 plural valent atoms selected from the groupconsisting of C, N, O, S and P that covalently attach the fluorogenic orfluorescent compounds to another moiety such as a chemically reactivegroup or a biological and non-biological component. The number of pluralvalent atoms in a linker may be, for example, 0, 1, 2, 3, 4, 5, 6, 7, 8,9, 10, 20, 25, 30 or a larger number up to 40 or more. A linker may belinear or non-linear; some linkers have pendant side chains or pendantfunctional groups, or both. Examples of such pendant moieties arehydrophilicity modifiers, for example solubilizing groups like, e.g.sulfo (—SO₃H or —SH₃ ⁻). In certain embodiments, L is composed of anycombination of single, double, triple or aromatic carbon-carbon bonds,carbon-nitrogen bonds, nitrogen-nitrogen bonds, carbon-oxygen bonds andcarbon-sulfur bonds. Exemplary linking members include a moiety thatincludes —C(O)NH—, —C(O)O—, —NH—, —S—, —O—, and the like. Linkers may,by way of example, consist of a combination of moieties selected fromalkyl; —C(O)NH—; —C(O)O—; —NH—; —S—; —O—; —C(O)—; —S(O)_(n)— where n is0, 1 or 2; —O—; 5- or 6- membered monocyclic rings; and optional pendantfunctional groups, for example sulfo, hydroxy and carboxy. The moietyformed by a linker bonded to a reactive group (R_(x)) may be designated-L-R_(x). The reactive group may be reacted with a substance reactivetherewith, whereby the linker becomes bonded to a conjugated substance(S_(c)) and may be designated -L-Sc, or in some cases, the linker maycontains a residue of a reactive group (e.g. the carbonyl group of anester) and may be designated “-L_(R)”. A “cleavable linker” is a linkerthat has one or more cleavable groups that may be broken by the resultof a reaction or condition. The term “cleavable group” refers to amoiety that allows for release of a portion, e.g., a fluorogenic orfluorescent moiety, of a conjugate from the remainder of the conjugateby cleaving a bond linking the released moiety to the remainder of theconjugate. Such cleavage is either chemical in nature, or enzymaticallymediated. Exemplary enzymatically cleavable groups include natural aminoacids or peptide sequences that end with a natural amino acid.

In addition to enzymatically cleavable groups, it is within the scope ofthe present invention to include one or more sites that are cleaved bythe action of an agent other than an enzyme. Exemplary non-enzymaticcleavage agents include, but are not limited to, acids, bases, light(e.g., nitrobenzyl derivatives, phenacyl groups, benzoin esters), andheat. Many cleavable groups are known in the art. See, for example, Junget al., Biochem. Biophys. Acta, 761:152-162 (1983); Joshi et al., J.Biol. Chem., 265:14518-14525 (1990); Zarling et al., J. Immunol.,124:913-920 (1980); Bouizar et al., Eur. J. Biochem., 155:141-147(1986); Park et al., J. Biol. Chem., 261:205-210 (1986); Browning etal., J. Immunol., 143:1859-1867 (1989). Moreover a broad range ofcleavable, bifunctional (both homo- and hetero-bifunctional) spacer armsare commercially available.

An exemplary cleavable group, such as an ester, is cleavable group thatmay be cleaved by a reagent, e.g., sodium hydroxide, resulting in acarboxylate-containing fragment and a hydroxyl-containing product.

The linker may be used to attach the pH-sensitive fluorescent dyecompound to another component of a conjugate, such as a targeting moiety(e.g., antibody, ligand, non-covalent protein-binding group, etc.), ananalyte, a biomolecule, a drug and the like.

In certain embodiments, compounds are provided in which -L- is of theformula -L1-(L2)_(p)-(L3)_(r)- wherein:

p is 0 or 1; r is 0 or 1; L1 is a bond, —CONH—, —COO—, or a moietycomprising at least two amino acids; L2 is —(CH₂)—,—CH₂CH₂O—(CH₂CH₂O)_(s)—CH₂CH₂—, or alkylene having from 1 to 30 carbonatoms and unsubstituted or substituted by at least one R^(a), e.g. 1, 2,3, 4, 5 or 6 R^(a); L3 is —CONH—(CH₂)_(t)—, —COO—(CH₂)_(t)— or a moietycomprising at least two amino acids, wherein:

-   -   r is from 1 to 30, e.g., 1 to 20 as in the case of 1 to 10, such        as 1, 2, 3, 4, 5 or 6; s is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10,        e.g., 1 to 7; t is from 1 to 30, e.g. 1 to 20 as in the case of        1 to 10, such as 1, 2, 3, 4, 5 or 6; R^(a) is sulfo (—SO₃H        and/or —SO₃ ⁻), hydroxy, carboxy or amino, particularly sulfo.

In certain embodiments, the total number of carbon atoms comprised inalkylene moieties in L is no more than 40, e.g., up to 35, 30, 25, 20,15 or 10. In certain embodiments, there is only a single one of L1 andL3 which comprises a moiety comprising at least two amino acids. Incertain embodiments, p and r are both 0. In certain embodiments, p is 1and r is 0. In certain embodiments, p and r are both 1.

In certain embodiments, L1 is a bond, —CONH— or —COO—. In certaincompounds L1 is a bond. In certain others, L1 is —CONH—.

L2, in certain embodiments, is —(CH₂)_(u)—, where u is from 1 to 10,e.g., 1, 2, 3, 4, 5 or 6. In certain embodiments, L2 is—CH₂CH₂O—(CH₂CH₂O)_(s)—CH₂CH₂— where s is from 1 to 7. In certainembodiments, L2 is alkylene having from 1 to 10 carbon atoms, e.g., 1,2, 3, 4, 5 or 6 carbon atoms, and which is unsubstituted or substitutedby 1, 2, 3, 4, 5 or 6 sulfo groups, e.g., 1 to 4 sulfo groups. For allL2 moieties mentioned in this paragraph, L1 is —CONH— in a particularclass of compounds. For all L2 moieties mentioned in this paragraph andall -L1-L2- combinations mentioned in this paragraph, r is 0 in oneclass of compounds.

In certain embodiments, (r+t) is from 1 to 30, e.g., 1 to 20 as in thecase of 1 to 10, such as 1, 2, 3, 4, 5 or 6, for example.

Exemplary linkers include, but are not limited to, the following: asingle covalent bond (for example between alkyl and a carboxy group orester of a carboxy group, or other reactive group); aminocarbonyl (forexample linking an alkyl group to a conjugated lipophilic moiety); aPEG-NH—CO-moiety (for example linking an alkyl group to an NHS-ester orother reactive group); an alkylaminocarbonyl group (for example linkingan alkyl group to an NHS-ester, amine or other reactive group); analkylaminocarbonyl group having a pendant group comprising sulfo—e.g. apendant sulfoalkyl group (for example linking an alkyl group toNHS-ester or other reactive group or to a lipophilic group); or a singlecovalent bond linking an alkyl group to a reactive group such as acarboxy group or ester thereof.

The terms “patient,” “subject” or “individual” refer to mammals andincludes humans and non-human mammals, such as monkeys, dogs, cats,pocket pets, horses, cows, pigs or rats.

The terms “protein” and “polypeptide” are used herein in a generic senseto include polymers of amino acid residues of any length. The term“peptide” is used herein to refer to polypeptides having less than 250amino acid residues, typically less than 100 amino acid residues. Theterms apply to amino acid polymers in which one or more amino acidresidues are an artificial chemical analogue of a correspondingnaturally occurring amino acid, as well as to naturally occurring aminoacid polymers.

The term “reactive group” (or “R_(x)”), as used herein, refers to agroup that is capable of reacting with another chemical group to form acovalent bond, i.e., is covalently reactive under suitable reactionconditions, and generally represents a point of attachment for anothersubstance. The reactive group is a moiety, such as carboxylic acid orsuccinimidyl ester, on the compounds of the present disclosure that iscapable of chemically reacting with a functional group on a differentcompound to form a covalent linkage. Reactive groups generally includenucleophiles, electrophiles and photoactivatable groups.

Exemplary reactive groups include, but not limited to, olefins,acetylenes, alcohols, phenols, ethers, oxides, halides, aldehydes,ketones, carboxylic acids, esters, amides, cyanates, isocyanates,thiocyanates, isothiocyanates, amines, hydrazines, hydrazones,hydrazides, diazo, diazonium, nitro, nitriles, mercaptans, sulfides,disulfides, sulfoxides, sulfones, sulfonic acids, sulfinic acids,acetals, ketals, anhydrides, sulfates, sulfenic acids isonitriles,amidines, imides, imidates, nitrones, hydroxylamines, oximes, hydroxamicacids thiohydroxamic acids, allenes, ortho esters, sulfites, enamines,ynamines, ureas, pseudoureas, semicarbazides, carbodiimides, carbamates,imines, azides, azo compounds, azoxy compounds, and nitroso compounds.Reactive functional groups also include those used to preparebioconjugates, e.g., N-hydroxysuccinimide esters, maleimides,succinimidyl esters (SE), sulfodichlorophenol (SDP) esters,sulfotetrafluorophenol (STP) esters, tetrafluorophenol (TFP) esters,acetoxymethoxy (AM) esters, nitrilotriacetic acids (NTA), aminodextrans,DIBO-amines and the like. Methods to prepare each of these functionalgroups are well known in the art and their application to ormodification for a particular purpose is within the ability of one ofskill in the art (see, for example, Sandler and Karo, eds., OrganicFunctional Group Preparations, Academic Press, San Diego, 1989).

The term “salt” refers to acceptable salts of a compound, which saltsare derived from a variety of organic and inorganic counter ions wellknown in the art and include, by way of example only, sodium, potassium,calcium, magnesium, ammonium, and tetraalkylammonium; and when themolecule contains a basic functionality, salts of organic or inorganicacids, such as hydrochloride, hydrobromide, tartrate, mesylate, acetate,maleate, and oxalate.

The term “sample,” as used herein, refers to any material that maycontain an analyte of interest or cells. Typically, the sample is a livecell or a biological fluid that comprises endogenous host cells.Alternatively, the sample may be a buffer solution or an environmentalsample for which pH determination is needed. The sample may be in anaqueous solution, a viable cell culture or immobilized on a solid orsemi-solid surface such as a polyacrylamide gel, membrane blot or on amicroarray.

The term “solid support,” as used herein, refers to a matrix or mediumthat is substantially insoluble in liquid phases and capable of bindinga molecule or particle of interest. Solid supports suitable for useherein include semi-solid supports and are not limited to a specifictype of support. Useful solid supports include solid and semi-solidmatrixes, such as aerogels and hydrogels, resins, beads, biochips(including thin film coated biochips), microfluidic chip, a siliconchip, multi-well plates (also referred to as microtitre plates ormicroplates), membranes, conducting and nonconducting metals, glass(including microscope slides) and magnetic supports. More specificexamples of useful solid supports include silica gels, polymericmembranes, particles, derivatized plastic films, glass beads, cotton,plastic beads, alumina gels, polysaccharides such as Sepharose®,poly(acrylate), polystyrene, poly(acrylamide), polyol, agarose, agar,cellulose, dextran, starch, FICOLL®, heparin, glycogen, amylopectin,mannan, inulin, nitrocellulose, diazocellulose, polyvinylchloride,polypropylene, polyethylene (including poly(ethylene glycol)), nylon,latex bead, magnetic bead, paramagnetic bead, superparamagnetic bead,starch and the like.

The terms “stereoisomer” or “stereoisomers” refer to compounds thatdiffer in the chirality of one or more stereocenters. Stereoisomersinclude enantiomers and diastereomers.

The term “tautomer” refers to alternate forms of a compound that differin the position of a proton, such as enol-keto and imine-enaminetautomers, or the tautomeric forms of heteroaryl groups containing aring atom attached to both a ring —NH— moiety and a ring ═N— moiety suchas pyrazoles, imidazoles, benzimidazoles, triazoles, and tetrazoles.

The terms “treating” or “treatment” of a disease in a patient referto 1) preventing the disease from occurring in a patient that ispredisposed or does not yet display symptoms of the disease; 2)inhibiting the disease or arresting its development; or 3) amelioratingor causing regression of the disease.

Dye Compounds and Compositions:

In general, for ease of understanding the present disclosure, thepH-sensitive fluorescent dye compounds and corresponding substituentswill first be described in detail, followed by various methods in whichthe pH-sensitive fluorescent dye compounds of the present invention areuseful, which is followed by exemplary methods of use and synthesis ofcertain novel pH-sensitive fluorescent dye compounds that areparticularly advantageous for use with the methods provided herein.

The pH-sensitive fluorescent dye compounds disclosed herein are usefulfor monitoring or detecting pH in a sample. For example, we have foundthat by introducing an electron donating group (EDG) into the4-amino-2-hydroxyphenyl ring of a fluorogenic pH-sensitive fluorescentdye compound that we were able to tune the fluorescent properties of thepH-sensitive fluorescent dye compound (See, structural formulae I andII). In particular we were able to tune the pKa value and obtain a pHsensitive compound with a pKa value compatible with live cellintracellular applications. We also found that replacing the hydroxyl atposition R₁ with an alkoxy or thioalkyl moiety not only increased thestability of the dye compounds in an aqueous environment but alsoresulted in a dye compound that was pH sensitive, an unexpectedadvantage in view of the teaching by Smith et al. (supra).Advantageously, the addition of a dialkylamino group to the anilinemoiety at position R³ resulted in the unexpected advantage of yieldingpKa values in the physiological range. In certain embodiments, thedialkylamino group is diethylamino. In certain embodiments, thedialkylamino group is dimethylamino.

In certain embodiments, the pKa value is about 6 to about 7. Withoutwishing to be bound by a theory, the pKa of the amino group of theaniline moiety of the compounds of structural formulae I and II appearsto depend on the ability of the aromatic system to share a lone electronpair on the oxygen atom. This ability is affected by additionalfunctional groups introduced into the aromatic system and thus, the pKais tuned by adding EDG groups to pH-sensitive dyes comprising anelectron rich aniline moiety.

In certain embodiments, the sample to be analyzed includes live cells ora biological fluid, including cytosol that comprises endogenous hostcell proteins, buffer solutions and environmental samples. Therefore,the pH-sensitive fluorescent dye compounds disclosed herein are usefulfor monitoring or determining pH changes and those events directly andindirectly associated with a change in pH. Monitoring of the pH may alsobe accomplished in live cells wherein the present pH-sensitivefluorescent dye compounds are internalized by live cells through anumber of different mechanisms, including both passive and cell mediatedmechanisms. For example, the present pH-sensitive fluorescent dyecompounds may comprise a lipophilic group such as an acetoxymethoxy (AM)or acetate ester that allows for entry across the live cell membrane.Once inside the cells, nonspecific esterases cleave the AM or acetateester resulting in a charged molecule that is well retained in the cell.Alternatively, the present pH-sensitive fluorescent dye compounds may beconjugated to a carrier molecule that allows the dye compound to betaken up by live cells. Examples include internalization duringphagocytosis, wherein the pH-sensitive fluorescent dye compounds areconjugated to bacterial particles or other proteins (or peptides) thatinduce phagocytosis by macrophages or monocytes; or up-take throughreceptor internalization when the present pH-sensitive fluorescent dyecompounds are conjugated to a carrier molecule that binds a receptor andthus induces internalization.

The pH-sensitive fluorescent dye compounds disclosed herein function asreporter molecules to confer a detectable signal, directly orindirectly, to the sample as a result of a change in pH. This results inthe ability to measure and monitor pH changes in a sample to directlyand indirectly detect specific events associated with a change in pH.

Where the detectable response is a fluorescence response, it istypically a change in fluorescence, such as a change in the intensity,excitation or emission wavelength, distribution of fluorescence,fluorescence lifetime, fluorescence polarization, or a combinationthereof. In certain embodiments, the detectable optical response uponprotonation is a change in fluorescence intensity that is greater thanapproximately 150% relative to the same dye compound wherein the anilinemoiety is not protonated on the nitrogen. Preferably, the change influorescence intensity is greater than 5-fold, and more preferably morethan 10-fold.

The pH-sensitive fluorescent dye compounds provided herein may comprisea fluorophore that may be any rhodamine or rhodol fluorophore, known toone skilled in the art, whose excitation and fluorescence is in thegreen portion of the UV/VIS spectrum. Preferably, the fluorophore isquenched, or substantially non-fluorescent, until the nitrogen on theaniline moiety is protonated.

.In certain embodiments, the pH-sensitive fluorescent dye compounds areindependently substituted by substituents selected from the groupconsisting of hydrogen, halogen, amino, substituted amino, alkyl,substituted alkyl, aryl, substituted aryl, heteroaryl, substitutedheteroaryl, alkoxy, sulfo, reactive group (R_(x)), conjugated substance(S_(c)), solid support and carrier molecule. In another embodiment, therhodamine and rhodol fluorophores disclosed herein comprise bothsubstituted and unsubstituted moieties on the carbon atom of the centralring of the xanthene by substituents typically found in thexanthene-based dyes such as phenyl and substituted-phenyl moieties. Mostpreferred dyes are rhodamine, rhodol, and derivatives thereof. Thechoice of the fluorophore attached to the aniline moiety will determinethe pH-sensitive compound's absorption and fluorescence emissionproperties as well as its live cell properties, i.e. ability to localizewithin a cell.

.In certain embodiments, the fluorophore (e.g., rhodamine or rhodol) isattached to the aniline moiety via a linker In certain embodiments, thefluorophore (and reactive group, carrier molecules, and solid support)comprises a linker that is used to covalently attach the substituents tothe aniline moieties disclosed herein. The fluorophore (and solidsupport, carrier molecule or reactive group) may be directly attached tothe moieties (where the linker is a single bond) or attached through aseries of stable bonds. Preferably the fluorophore is directly attachedby a single covalent bond to the aniline moiety, but may also beattached via a linker as described below for reactive group, carriermolecules, and solid support. When the linker is a series of stablecovalent bonds the linker typically incorporates 1-30 nonhydrogen atomsselected from the group consisting of C, N, O, S and P. When the linkeris not a single covalent bond, the linker may be any combination ofstable chemical bonds, optionally including, single, double, triple oraromatic carbon-carbon bonds, as well as carbon-nitrogen bonds,nitrogen-nitrogen bonds, carbon-oxygen bonds, sulfur-sulfur bonds,carbon-sulfur bonds, phosphorus-oxygen bonds, phosphorus-nitrogen bonds,and nitrogen-platinum bonds. Typically the linker incorporates less than15 nonhydrogen atoms and are composed of any combination of ether,thioether, thiourea, amine, ester, carboxamide, sulfonamide, hydrazidebonds and aromatic or heteroaromatic bonds. Typically the linker is acombination of single carbon-carbon bonds and carboxamide, sulfonamideor thioether bonds. The bonds of the linker typically result in thefollowing moieties that may be found in the linker ether, thioether,carboxamide, thiourea, sulfonamide, urea, urethane, hydrazine, alkyl,aryl, heteroaryl, alkoxy, cycloalkyl and amine moieties. Examples of alinker include, but are not limited to, substituted or unsubstitutedpolymethylene, arylene, alkylarylene, arylenealkyl, or arylthio.

In certain embodiments, the linker contains 1-6 carbon atoms. In certainembodiments, the linker comprises a thioether linkage. Exemplary linkingmembers include a moiety that includes, but is not limited to, —C(O)NH—,—C(O)O—, —NH—, —S—, —O—, and the like. In certain embodiments, thelinker is or incorporates the formula —(CH₂)_(d)(CONH(CH₂)_(e))_(z)—, orwhere d is an integer from 0 to 5, e is an integer from 1 to 5 and z is0 or 1. In certain embodiments, the linker is or incorporates theformula —O(CH₂)—. In certain embodiments, the linker is or incorporatesa phenylene or a 2-carboxy-substituted phenylene.

.Any combination of linkers may be used to attach the carrier molecule,solid support or reactive group and the present pH-sensitive fluorescentdye compounds together. The linker may also be substituted to alter thephysical properties of the fluorophore or aniline moiety, such asspectral properties of the pH-sensitive fluorescent dye compounds.

Another important feature of the linker is to provide an adequate spacebetween the carrier molecule, reactive group or solid support and theaniline moiety or fluorophore so as to prevent steric hindrance.Therefore, the linker of the pH-sensitive fluorescent dye compoundsdisclosed herein is important for (1) attaching the carrier molecule,reactive group or solid support to the dye compounds and attaching thefluorophore to the aniline moiety, (2) providing an adequate spacebetween the carrier molecule, reactive group or solid support and thedye compound so as not to sterically hinder the action of the compoundand (3) for altering the physical properties of the dye compoundsdisclosed herein.

The pH sensing or electron rich aniline moiety of the pH-sensitivefluorescent dye compounds disclosed herein is any moiety that, whenprotonated, results in the compound being fluorescent, whilst thecompound is quenched when the aniline moiety is not in the protonatedstate. The pH-sensitive fluorescent dye compounds often have a pKa valuein the range of about 2 to about 10. In certain embodiments the pKa ofthe pH-sensitive fluorescent dye compound is about 3 to about 10. Incertain embodiments, the pKa of the pH-sensitive fluorescent dyecompound is about 5 to about 8. In certain embodiments the pKa of thepH-sensitive fluorescent dye compound is about 6 to about 8. In certainembodiments the pKa of the pH-sensitive fluorescent dye compound isabout 6 to about 7. In certain embodiment the pKa of the pH-sensitivefluorescent dye compound is about 6.5. Preferably the pKa of thepH-sensitive fluorescent dye compounds provided herein is about 6 toabout 7.

To tune the pKa to about 6 to about 7, electron donating groups (EDG)were introduced into the aniline moiety on the aryl group. This combinedwith the presence of an alkoxy or other like substituents on the arylwhen a —OH or —SH were not present, unexpectedly resulted inpH-sensitive fluorescent dye compounds that were stable in an aqueousenvironment and provided a pKa in the desired range. As disclosed in andwith reference to the formulae herein, the amino group of the anilinemoiety may be substituted or replaced by another basic moiety of higherpKa. Advantageously, the addition of a dialkylamino group, wherein eachof the alkyl groups, which may be the same or different, isindependently alkyl or substituted alkyl, to the aniline group atposition R³ resulted in the unexpected advantage of yielding pKa valuesin the physiological range. In certain embodiments, the dialkylaminogroup is dimethylamino. In certain embodiments, the dialkylamino groupis diethylamino.

In certain embodiments, without wishing to be bound by a theory, thefunctioning of the pH-sensitive fluorescent dye compounds providedherein as a pH indicator is illustrated below in Scheme 2:

wherein X is a fluorophore and R⁴ and R⁵ are as described previouslyherein.

The EDG is typically at R³, but may be located at any position on thearyl group. Electron donating groups of the present invention include,for example, alkoxy, substituted alkoxy, amino, substituted amino,dialkylamino, halogen, alkylthio, acylamino, and (carboxyl ester)oxy.Preferred EDGs are —OCH₃, —NH₂, —NHCH₃, —N(CH₃)₂, and —N(CH₂CH₃)₂. Incertain embodiments, Z is O-alkyl. In certain embodiments, Z isthioalkyl.

In certain embodiments, novel dye compounds are provided for use asfluorescent pH sensors, the dye compounds having structural formula (I):

wherein

R₁ is alkoxy or thioalkyl;

R² and R⁶, which may be the same or different, are each independently H,halogen, —OR^(a), —SR^(a), —NR^(a)R^(b), or an electron donating group;

R³ is —NR′R″, wherein R′ and R″, which may be the same or different, areeach independently alkyl or substituted alkyl;

R⁴ is selected from the group consisting of alkyl and substituted alkyl;

R⁵ is selected from the group consisting of alkyl; substituted alkyl;alkenyl; substituted alkenyl; acyl; aryl; substituted aryl;carboxyalkyl; heteroaryl; substituted heteroaryl; heterocyclyl;substituted heterocyclyl; alkylcarboxy; alkylalkoxycarbonyl;alkylaminocarbonyl; alkylaryloxycarbonyl; alkylheteroaryl;(CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NNR^(c);wherein n is an integer from 1 to 6, and R and R^(c), which may be thesame or different, are each independently H, alkyl, substituted alkyl,aryl, substituted aryl, heteroaryl, substituted heteroaryl, substitutedamino, alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilicgroup, or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is aninteger from 1 to 6, and R_(x) is a reactive group; -L-R_(x); and-L-S_(c), wherein L is a linker, R_(x) is a reactive group, and S_(c) isa conjugated substance;

R^(a) is H, alkyl, or substituted alkyl; and

R^(b) is alkyl or substituted alkyl.

In certain embodiments, R₁-R⁶ are as follows:

R₁ is alkoxy or thioalkyl;

R² and R⁶, which may be the same or different, are each independently Hor halogen;

R³ is —NR′R″, wherein R′ and R″, which may be the same or different, areeach independently alkyl;

R⁴ is alkyl; and

R⁵ is selected from the group consisting of alkyl; substituted alkyl;alkenyl; substituted alkenyl; acyl; aryl; substituted aryl;carboxyalkyl; heteroaryl; substituted heteroaryl; heterocyclyl;substituted heterocyclyl; alkylcarboxy; alkylalkoxycarbonyl;alkylaminocarbonyl; alkylaryloxycarbonyl; alkylheteroaryl;(CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NNR^(c);wherein n is an integer from 1 to 6, and R and R^(c), which may be thesame or different, are each independently H, alkyl, substituted alkyl,aryl, substituted aryl, heteroaryl, substituted heteroaryl, substitutedamino, alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilicgroup, or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is aninteger from 1 to 6, and R_(x) is a reactive group; -L-R_(x); and-L-S_(c).

In certain embodiments, R₁-R⁶ are as follows:

R₁ is alkoxy or thioalkyl;

R² and R⁶, which may be the same or different, are each independently H,Cl or F;

R³ is —NR′R″, wherein R′ and R″, which may be the same or different, areeach independently alkyl;

R⁴ is alkyl; and

R⁵ is selected from the group consisting of alkyl; substituted alkyl;alkenyl; substituted alkenyl; acyl; aryl; substituted aryl;carboxyalkyl; heteroaryl; substituted heteroaryl; heterocyclyl;substituted heterocyclyl; alkylcarboxy; alkylalkoxycarbonyl;alkylaminocarbonyl; alkylaryloxycarbonyl; alkylheteroaryl;(CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NNR^(c);wherein n is an integer from 1 to 6, and R and R^(c), which may be thesame or different, are each independently H, alkyl, substituted alkyl,aryl, substituted aryl, heteroaryl, substituted heteroaryl, substitutedamino, alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilicgroup, or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is aninteger from 1 to 6, and R_(x) is a reactive group; -L-R_(x); and-L-S_(c).

In certain embodiments, R₁-R⁶ are as follows:

R₁ is alkoxy or thioalkyl;

R² and R⁶ are each H;

R³ is —NR′R″, wherein R′ and R″, which may be the same or different, areeach independently alkyl;

R⁴ is alkyl; and

R⁵ is selected from the group consisting of alkyl; substituted alkyl;alkenyl; substituted alkenyl; acyl; aryl; substituted aryl;carboxyalkyl; heteroaryl; substituted heteroaryl; heterocyclyl;substituted heterocyclyl; alkylcarboxy; alkylalkoxycarbonyl;alkylaminocarbonyl; alkylaryloxycarbonyl; alkylheteroaryl;(CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NNR^(c);wherein n is an integer from 1 to 6, and R and R^(c), which may be thesame or different, are each independently H, alkyl, substituted alkyl,aryl, substituted aryl, heteroaryl, substituted heteroaryl, substitutedamino, alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilicgroup, or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is aninteger from 1 to 6, and R_(x) is a reactive group; -L-R_(x); and-L-S_(c).

In certain embodiments, R₁-R⁶ are as follows:

R₁ is methoxy;

R² and R⁶ are each H;

R³ is —NR′R″, wherein R′ and R″, which may be the same or different, areeach independently methyl or ethyl;

R⁴ is methyl or ethyl; and

R⁵ is methyl; ethyl; carboxyalkyl; (CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R;(CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NRR^(c); wherein n is an integer from 1to 6, and R and R^(c), which may be the same or different, are eachindependently H, alkyl, substituted alkyl, aryl, substituted aryl,heteroaryl, substituted heteroaryl, substituted amino,alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilic group,or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is an integerfrom 1 to 6, and R_(x) is a reactive group selected from carboxyl,carboxylester, amide, maleimide, succinimidyl ester (SE),sulfodichlorophenol (SDP) ester, sulfotetrafluorophenol (STP) ester,tetrafluorophenol (TFP) ester, acetoxymethoxy (AM) ester,nitrilotriacetic acid (NTA), aminodextran, DIBO-amine; -L-R_(x); or-L-S_(c).

In certain embodiments, novel dye compounds are provided for use asfluorescent pH sensors having structural formula (II):

wherein

R₁ is alkoxy or thioalkyl;

R² and R⁶, which may be the same or different, are each independently H,halogen, —OR^(a), —SR^(a), —NR^(a)R^(b), or an electron donating group;

R³ is —NR′R″, wherein R′ and R″, which may be the same or different, areeach independently alkyl or substituted alkyl;

R⁴ is selected from the group consisting of alkyl and substituted alkyl;

R⁵ is selected from the group consisting of alkyl; substituted alkyl;alkenyl; substituted alkenyl; acyl; aryl; substituted aryl;carboxyalkyl; heteroaryl; substituted heteroaryl; heterocyclyl;substituted heterocyclyl; alkylcarboxy; alkylalkoxycarbonyl;alkylaminocarbonyl; alkylaryloxycarbonyl; alkylheteroaryl;(CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NNR^(c);wherein n is an integer from 1 to 6, and R and R^(c), which may be thesame or different, are each independently H, alkyl, substituted alkyl,aryl, substituted aryl, heteroaryl, substituted heteroaryl, substitutedamino, alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilicgroup, or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is aninteger from 1 to 6, and R_(x) is a reactive group; -L-R_(x); and-L-S_(c), wherein L is a linker, R_(x) is a reactive group, and S_(c) isa conjugated substance;

R^(a) is H, alkyl, or substituted alkyl; and

R^(b) is alkyl or substituted alkyl.

In certain embodiments, R₁-R⁶ are as follows:

R₁ is alkoxy or thioalkyl;

R² and R⁶, which may be the same or different, are each independently Hor halogen;

R³ is —NR′R″, wherein R′ and R″, which may be the same or different, areeach independently alkyl;

R⁴ is alkyl; and

R⁵ is selected from the group consisting of alkyl; substituted alkyl;alkenyl; substituted alkenyl; acyl; aryl; substituted aryl;carboxyalkyl; heteroaryl; substituted heteroaryl; heterocyclyl;substituted heterocyclyl; alkylcarboxy; alkylalkoxycarbonyl;alkylaminocarbonyl; alkylaryloxycarbonyl; alkylheteroaryl;(CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NNR^(c);wherein n is an integer from 1 to 6, and R and R^(c), which may be thesame or different, are each independently H, alkyl, substituted alkyl,aryl, substituted aryl, heteroaryl, substituted heteroaryl, substitutedamino, alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilicgroup, or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is aninteger from 1 to 6, and R_(x) is a reactive group; -L-R_(x); and-L-S_(c).

In certain embodiments, R₁-R⁶ are as follows:

R₁ is alkoxy or thioalkyl;

R² and R⁶, which may be the same or different, are each independently H,Cl or F;

R³ is —NR′R″, wherein R′ and R″, which may be the same or different, areeach independently alkyl;

R⁴ is alkyl; and

R⁵ is selected from the group consisting of alkyl; substituted alkyl;alkenyl; substituted alkenyl; acyl; aryl; substituted aryl;carboxyalkyl; heteroaryl; substituted heteroaryl; heterocyclyl;substituted heterocyclyl; alkylcarboxy; alkylalkoxycarbonyl;alkylaminocarbonyl; alkylaryloxycarbonyl; alkylheteroaryl;(CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NNR^(c);wherein n is an integer from 1 to 6, and R and R^(c), which may be thesame or different, are each independently H, alkyl, substituted alkyl,aryl, substituted aryl, heteroaryl, substituted heteroaryl, substitutedamino, alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilicgroup, or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is aninteger from 1 to 6, and R_(x) is a reactive group; -L-R_(x); and-L-S_(c).

In certain embodiments, R₁-R⁶ are as follows:

R₁ is alkoxy or thioalkyl;

R² and R⁶ are each H;

R³ is —NR′R″, wherein R′ and R″, which may be the same or different, areeach independently alkyl;

R⁴ is alkyl; and

R⁵ is selected from the group consisting of alkyl; substituted alkyl;alkenyl; substituted alkenyl; acyl; aryl; substituted aryl;carboxyalkyl; heteroaryl; substituted heteroaryl; heterocyclyl;substituted heterocyclyl; alkylcarboxy; alkylalkoxycarbonyl;alkylaminocarbonyl; alkylaryloxycarbonyl; alkylheteroaryl;(CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NNR^(c);wherein n is an integer from 1 to 6, and R and R^(c), which may be thesame or different, are each independently H, alkyl, substituted alkyl,aryl, substituted aryl, heteroaryl, substituted heteroaryl, substitutedamino, alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilicgroup, or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is aninteger from 1 to 6, and R_(x) is a reactive group; -L-R_(x); and-L-S_(c).

In certain embodiments, R₁-R⁶ are as follows:

R₁ is methoxy;

R² and R⁶ are each H;

R³ is —NR′R″, wherein R′ and R″, which may be the same or different, areeach independently methyl or ethyl;

R⁴ is methyl or ethyl; and

R⁵ is methyl; ethyl; carboxyalkyl; (CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R;(CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NRR^(c); wherein n is an integer from 1to 6, and R and R^(c), which may be the same or different, are eachindependently H, alkyl, substituted alkyl, aryl, substituted aryl,heteroaryl, substituted heteroaryl, substituted amino,alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilic group,or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is an integerfrom 1 to 6, and R_(x) is a reactive group selected from carboxyl,carboxylester, amide, maleimide, succinimidyl ester (SE),sulfodichlorophenol (SDP) ester, sulfotetrafluorophenol (STP) ester,tetrafluorophenol (TFP) ester, acetoxymethoxy (AM) ester,nitrilotriacetic acid (NTA), aminodextran, DIBO-amine; -L-R_(x); or-L-S_(c).

In certain embodiments, the EDG is selected from the group consisting ofalkoxy, substituted alkoxy, amino, substituted amino, halogen,alkylthio, acylamino, and (carboxyl ester)oxy. In certain embodiments,the EDG is not hydroxy or thiol. In certain embodiments, the EDG is adialkylamino group. In certain embodiments, the dialkylamino group isdimethylamino or diethylamino.

In certain embodiments, R₁ is —OCH₃ and R³ is —N(CH₃)₂ or —N(CH₂CH₃)₂.

In certain embodiments, R⁴ and R⁵ are alkyl or substituted alkyl. Incertain embodiments, R⁵ is methyl; ethyl; carboxyalkyl; (CH₂)_(n)CO(O)R;(CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NRR^(c); wherein n is aninteger from 1 to 6, and R and R^(c), which may be the same ordifferent, are each independently H, alkyl, substituted alkyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, substituted amino,alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilic group,or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is an integerfrom 1 to 6, and R_(x) is a reactive group selected from carboxyl,carboxylester, amide, maleimide, succinimidyl ester (SE),sulfodichlorophenol (SDP) ester, sulfotetrafluorophenol (STP) ester,tetrafluorophenol (TFP) ester, acetoxymethoxy (AM) ester,nitrilotriacetic acid (NTA), aminodextran, DIBO-amine; -L-R_(x); or-L-S_(c).

In certain embodiments of any of the previous embodiments, the pKa ofthe pH-sensitive fluorescent dye compound is about 5 to about 8. Incertain embodiments, the pKa of the pH-sensitive fluorescent dyecompound is about 6 to about 8. In certain embodiments, the pKa of thepH-sensitive fluorescent dye compound is about 6 to about 7. In certainembodiments, the pKa of the pH-sensitive fluorescent dye compound isabout 6.5. In certain embodiments, the pKa of the pH-sensitivefluorescent dye compound is about 3 to about 10.

The 4-position nitrogen of the aniline or aniline-like ring of thecompounds disclosed herein does of course always have a permissiblevalency.

Reactive Groups:

In certain embodiments, the pH-sensitive fluorescent dye compoundsprovided herein are chemically reactive, and are substituted by at leastone reactive group (R_(x)). The reactive group functions as the site ofattachment for another moiety, such as a carrier molecule or a solidsupport, wherein the reactive group chemically reacts with anappropriate reactive or functional group on the carrier molecule orsolid support. Thus, in certain embodiments, the pH-sensitivefluorescent dye compounds provided herein comprise an aniline moiety,linker, fluorophore, a reactive group moiety and optionally a carriermolecule and/or a solid support.

In certain embodiments, the pH-sensitive fluorescent dye compoundsprovided herein further comprise a reactive group which is a memberselected from an acrylamide, an activated ester of a carboxylic acid, acarboxylic ester, an acyl azide, an acyl nitrile, an aldehyde, an alkylhalide, an anhydride, an aniline, an amine, an aryl halide, an azide, anaziridine, a boronate, a diazoalkane, a haloacetamide, a haloalkyl, ahalotriazine, a hydrazine, an imido ester, an isocyanate, anisothiocyanate, a maleimide, a phosphoramidite, a photoactivatablegroup, a reactive platinum complex, a silyl halide, a sulfonyl halide,and a thiol. In certain embodiments the reactive group is selected fromthe group consisting of carboxylic acid, succinimidyl ester of acarboxylic acid, hydrazide, amine and a maleimide. The reactive groupmay be attached to any appropriate site on the reporter molecule or theaniline moiety. In certain embodiments, at least one member selectedfrom R¹, R², R³, R⁴, R⁵, and R⁶ is a reactive group. Preferably, atleast one of R³, R⁴, R⁵, and R⁶ is a reactive group, most preferred isat least one of R⁴ or R⁵. Alternatively, if the pH-sensitive fluorescentdye compounds disclosed herein comprise a carrier molecule or solidsupport a reactive group may be covalently attached independently tothose substituents, allowing for further conjugation to a fluorophore,carrier molecule or solid support.

These reactive groups are synthesized during the formation of thepH-sensitive fluorescent dye compounds provided herein and carriermolecule- and/or solid support-containing compounds to providechemically reactive pH-sensitive fluorescent dye compounds. In this way,pH-sensitive fluorescent dye compounds incorporating a reactive groupmay be covalently attached to a wide variety of carrier molecules orsolid supports that contain, or are modified to contain, functionalgroups with suitable reactivity, resulting in chemical attachment of thecomponents. In certain embodiments, the reactive group of thepH-sensitive fluorescent dye compounds disclosed herein and thefunctional group of the carrier molecule or solid support compriseelectrophiles and nucleophiles that can generate a covalent linkagebetween them. In certain embodiments, the reactive group comprises aphotoactivatable group, which becomes chemically reactive only afterillumination with light of an appropriate wavelength. Typically, theconjugation reaction between the reactive group and the carrier moleculeor solid support results in one or more atoms of the reactive groupbeing incorporated into a new linkage attaching the pH-sensitivefluorescent dye compounds disclosed herein to the carrier molecule orsolid support. Selected examples of functional groups and linkages areshown in Table 2, where the reaction of an electrophilic group and anucleophilic group yields a covalent linkage.

TABLE 2 Examples of some routes to useful covalent linkagesElectrophilic Group Nucleophilic Group Resulting Covalent Linkageactivated esters* amines/anilines carboxamides acrylamides thiolsthioethers acyl azides** amines/anilines carboxamides acyl halidesamines/anilines carboxamides acyl halides alcohols/phenols esters acylnitriles alcohols/phenols esters acyl nitriles amines/anilinescarboxamides aldehydes amines/anilines imines aldehydes or ketoneshydrazines hydrazones aldehydes or ketones hydroxylamines oximes alkylhalides amines/anilines alkyl amines alkyl halides carboxylic acidsesters alkyl halides thiols thioethers alkyl halides alcohols/phenolsethers alkyl sulfonates thiols thioethers alkyl sulfonates carboxylicacids esters alkyl sulfonates alcohols/phenols ethers anhydridesalcohols/phenols esters anhydrides amines/anilines carboxamides arylhalides thiols thiophenols aryl halides amines aryl amines aziridinesthiols thioethers boronates glycols boronate esters carbodiimidescarboxylic acids N-acylureas or anhydrides diazoalkanes carboxylic acidsesters epoxides thiols thioethers haloacetamides thiols thioethershaloplatinate amino platinum complex haloplatinate heterocycle platinumcomplex haloplatinate thiol platinum complex halotriazinesamines/anilines aminotriazines halotriazines alcohols/phenols triazinylethers halotriazines thiols triazinyl thioethers imido estersamines/anilines amidines isocyanates amines/anilines ureas isocyanatesalcohols/phenols urethanes isothiocyanates amines/anilines thioureasmaleimides thiols thioethers phosphoramidites alcohols phosphite esterssilyl halides alcohols silyl ethers sulfonate esters amines/anilinesalkyl amines sulfonate esters thiols thioethers sulfonate esterscarboxylic acids esters sulfonate esters alcohols ethers sulfonylhalides amines/anilines sulfonamides sulfonyl halides phenols/alcoholssulfonate esters *Activated esters, as understood in the art, generallyhave the formula —COΩ, where Ω is a suitable leaving group (e.g.,succinimidyloxy (—OC₄H₄O₂), sulfosuccinimidyloxy (—OC₄H₃O₂—SO₃H),-1-oxybenzotriazolyl (—OC₆H₄N₃); or an aryloxy group or aryloxysubstituted one or more times by electron withdrawing substituents suchas nitro, fluoro, chloro, cyano, or trifluoromethyl, or combinationsthereof, used to form activated aryl esters; or a carboxylic acidactivated by a carbodiimide to form an anhydride or mixed anhydride—OCOR^(x) or —OCNR^(x)NHR^(y), where R^(x) and R^(y), which may be thesame or different, are C₁-C₆ alkyl, C₁-C₆ perfluoroalkyl, or C₁-C₆alkoxy; or cyclohexyl, 3-dimethylaminopropyl, or N-morpholinoethyl).**Acyl azides can also rearrange to isocyanates.

The choice of the reactive group used to attach the pH-sensitivefluorescent dye compounds disclosed herein to the substance to beconjugated typically depends on the reactive or functional group on thesubstance to be conjugated and the type or length of covalent linkagedesired. The types of functional groups typically present on the organicor inorganic substances (biomolecule or non-biomolecule) include, butare not limited to, amines, amides, thiols, alcohols, phenols,aldehydes, ketones, phosphates, imidazoles, hydrazines, hydroxylamines,disubstituted amines, halides, epoxides, silyl halides, carboxylateesters, sulfonate esters, purines, pyrimidines, carboxylic acids,olefinic bonds, or a combination of these groups. A single type ofreactive site may be available on the substance (typical forpolysaccharides or silica), or a variety of sites may occur (e.g.,amines, thiols, alcohols, phenols), as is typical for proteins.

Typically, the reactive group will react with an amine, a thiol, analcohol, an aldehyde, a ketone, or with silica. Preferably, reactivegroups react with an amine or a thiol functional group, or with silica.In certain embodiments, the reactive group is an acrylamide, anactivated ester of a carboxylic acid, an acyl azide, an acyl nitrile, analdehyde, an alkyl halide, a silyl halide, an anhydride, an aniline, anaryl halide, an azide, an aziridine, a boronate, a diazoalkane, ahaloacetamide, a halotriazine, a hydrazine (including hydrazides), animido ester, an isocyanate, an isothiocyanate, a maleimide, aphosphoramidite, a reactive platinum complex, a sulfonyl halide, or athiol group. As used herein, “reactive platinum complex” refers tochemically reactive platinum complexes such as described in U.S. Pat.No. 5,714,327, herein incorporated by reference in its entirety.

In certain embodiments, the pH-sensitive fluorescent dye compoundsdisclosed herein comprise at least one reactive group that selectivelyreacts with an amine group. This amine-reactive group is selected fromthe group consisting of succinimidyl ester (SE), sulfonyl halide,tetrafluorophenyl (TFP) ester, sulfodichlorophenol (SDP) ester,sulfotetrafluorophenol (STP) ester, acetoxymethoxy (AM) ester,nitrilotriacetic acid (NTA), aminodextran, DIBO-amine andiosothiocyanates. Thus, in certain embodiments, the pH-sensitivefluorescent dye compounds provided herein form a covalent bond with anamine containing molecule in a sample. In certain embodiments, thepH-sensitive fluorescent dye compounds provided herein comprise at leastone reactive group that selectively reacts with a thiol group. Thisthiol-reactive group is selected from the group consisting of maleimide,haloalkyl and haloacetamide (including any reactive groups disclosed inU.S. Pat. Nos. 5,362,628; 5,352,803 and 5,573,904, all of which areherein incorporated by reference in their entirety).

Where the reactive group is an activated ester of a carboxylic acid,such as a succinimidyl ester of a carboxylic acid, a sulfonyl halide,tetrafluorophenyl (TFP) ester, sulfodichlorophenol (SDP) ester,sulfotetrafluorophenol (STP) ester, acetoxymethoxy (AM) ester,nitrilotriacetic acid (NTA), aminodextran, DIBO-amine or anisothiocyanate, the resulting pH-sensitive fluorescent dye compound isparticularly useful for preparing conjugates of carrier molecules suchas proteins, nucleotides, oligonucleotides, or haptens. Where thereactive group is a maleimide, haloalkyl or haloacetamide (including anyreactive groups disclosed in U.S. Pat. Nos. 5,362,628; 5,352,803 and5,573,904, all of which are herein incorporated by reference in theirentirety) the resulting compound is particularly useful for conjugationto thiol-containing substances. Where the reactive group is a hydrazide,the resulting compound is particularly useful for conjugation toperiodate-oxidized carbohydrates and glycoproteins, and in addition isan aldehyde-fixable polar tracer for cell microinjection. Where thereactive group is a silyl halide, the resulting compound is particularlyuseful for conjugation to silica surfaces, particularly where the silicasurface is incorporated into a fiber optic probe subsequently used forremote ion detection or quantitation.

In a certain embodiments, the reactive group is a photoactivatable groupsuch that the group is only converted to a reactive species afterillumination with an appropriate wavelength. An appropriate wavelengthis generally a UV wavelength that is less than 400 nm. This methodprovides for specific attachment to only the target molecules, either insolution or immobilized on a solid or semi-solid matrix.Photoactivatable reactive groups include, without limitation,benzophenones, aryl azides and diazirines.

Preferably, the reactive group is a photoactivatable group, succinimidylester of a carboxylic acid, a haloacetamide, haloalkyl, a hydrazine, anisothiocyanate, a maleimide group, an aliphatic amine, a silyl halide, acadaverine or a psoralen. More preferably, the reactive group is asuccinimidyl ester of a carboxylic acid, a maleimide, an iodoacetamide,or a silyl halide. In certain embodiments, the reactive group is asuccinimidyl ester of a carboxylic acid, a sulfonyl halide, atetrafluorophenyl ester, an iosothiocyanates or a maleimide. In certainembodiments, the reactive group is selected from sulfodichlorophenyl(SDP) ester, sulfotetrafluorophenol (STP) ester, tetrafluorophenol (TFP)ester, an acetoxymethoxy (AM) ester, and a nitrilotriacetic acid (NTA).

Carrier Molecules:

In certain embodiments, the pH-sensitive fluorescent dye compoundsprovided herein are covalently bound to a carrier molecule. If thepH-sensitive fluorescent dye compound has a reactive group, then thecarrier molecule may alternatively be linked to the pH-sensitivefluorescent dye compound through the reactive group. The reactive groupmay contain both a reactive functional moiety and a linker, or only thereactive functional moiety.

A variety of carrier molecules are useful herein. Exemplary carriermolecules include antigens, steroids, vitamins, drugs, haptens,metabolites, toxins, environmental pollutants, amino acids, peptides,proteins, nucleic acids, nucleic acid polymers, carbohydrates, lipids,polymers and bacterial particles. In certain embodiments, at least onemember selected from R¹, R², R³, R⁴, R⁵, and R⁶ is a carrier molecule.Preferably, at least one of R³, R⁴, R⁵, and R⁶ is a carrier molecule,most preferred is at least one of R⁴ or R⁵.

In certain embodiments, the carrier molecule comprises an amino acid, apeptide, a protein, a polysaccharide, a nucleoside, a nucleotide, anoligonucleotide, a nucleic acid, a hapten, a psoralen, a drug, ahormone, a lipid, a lipid assembly, a synthetic polymer, a polymericmicroparticle, a biological cell, a virus and combinations thereof. Incertain embodiments, the carrier molecule is selected from a hapten, anucleotide, an oligonucleotide, a nucleic acid polymer, a protein, apeptide or a polysaccharide. In certain embodiments the carrier moleculeis amino acid, a peptide, a protein, a polysaccharide, a nucleoside, anucleotide, an oligonucleotide, a nucleic acid, a hapten, a psoralen, adrug, a hormone, a lipid, a lipid assembly, a tyramine, a syntheticpolymer, a polymeric microparticle, a biological cell, cellularcomponents, an ion chelating moiety, an enzymatic substrate or a virus.In certain embodiments, the carrier molecule is an antibody or fragmentthereof, an antigen, an avidin or streptavidin, a biotin, a dextran, anIgG binding protein, a fluorescent protein, agarose, and anon-biological microparticle. In certain embodiments, carrier moleculesmay comprise a label or a fluorescent dye or quencher.

In certain embodiments, the carrier molecule is an amino acid (includingthose that are protected or are substituted by phosphates,carbohydrates, or C₁ to C₂₂ carboxylic acids), or a polymer of aminoacids such as a peptide or protein. In certain embodiments, the carriermolecule contains at least five amino acids, more preferably 5 to 36amino acids. Exemplary peptides include, but are not limited to,neuropeptides, cytokines, toxins, protease substrates, and proteinkinase substrates. Other exemplary peptides may function as organellelocalization peptides, that is, peptides that serve to target theconjugated compound for localization within a particular cellularsubstructure by cellular transport mechanisms. Preferred protein carriermolecules include enzymes, antibodies, lectins, glycoproteins, histones,albumins, lipoproteins, avidin, streptavidin, protein A, protein G,phycobiliproteins and other fluorescent proteins, hormones, toxins andgrowth factors. Typically, the protein carrier molecule is an antibody,an antibody fragment, avidin, streptavidin, a toxin, a lectin, a growthfactor, bacterial particle or a binding partner for a cell receptor.

In certain embodiments, the carrier molecule comprises a nucleic acidbase, nucleoside, nucleotide or a nucleic acid polymer, optionallycontaining an additional linker or spacer for attachment of afluorophore or other ligand, such as an alkynyl linkage (U.S. Pat. No.5,047,519), an aminoallyl linkage (U.S. Pat. No. 4,711,955) or otherlinkage. In certain embodiments, the nucleotide carrier molecule is anucleoside or a deoxynucleoside or a dideoxynucleoside.

Exemplary nucleic acid polymer carrier molecules are single- ormulti-stranded, natural or synthetic DNA or RNA oligonucleotides, orDNA/RNA hybrids, or incorporating an unusual linker such as morpholinederivatized phosphates (AntiVirals, Inc., Corvallis Oreg.), or peptidenucleic acids such as N-(2-aminoethyl)glycine units, where the nucleicacid contains fewer than 50 nucleotides, more typically fewer than 25nucleotides.

In certain embodiments, the carrier molecule comprises a carbohydrate orpolyol that is typically a polysaccharide, such as dextran, FICOLL®,heparin, glycogen, amylopectin, mannan, inulin, starch, agarose andcellulose, or is a polymer such as a poly(ethylene glycol). In certainembodiments, the polysaccharide carrier molecule includes dextran,agarose or FICOLL®.

In certain embodiments, the carrier molecule comprises a lipid(typically having 6-25 carbons), including glycolipids, phospholipids,and sphingolipids. In certain embodiments, the carrier moleculecomprises a lipid vesicle, such as a liposome, or is a lipoprotein. Somelipophilic substituents are useful for facilitating transport of theconjugated dye into cells or cellular organelles.

In certain embodiments, the carrier molecule is a cell, cellular system,cellular fragment, or subcellular particles, including virus particles,bacterial particles, virus components, biological cells (such as animalcells, plant cells, bacteria, or yeast), or cellular components.Examples of cellular components that are useful as carrier moleculesinclude lysosomes, endosomes, cytoplasm, nuclei, histones, mitochondria,Golgi apparatus, endoplasmic reticulum and vacuoles.

In certain embodiments, the carrier molecule non-covalently associateswith organic or inorganic materials. Exemplary embodiments of thecarrier molecule that possess a lipophilic substituent may be used totarget lipid assemblies such as biological membranes or liposomes bynon-covalent incorporation of the pH-sensitive fluorescent dye compoundwithin the membrane, e.g., for use as probes for membrane structure orfor incorporation in liposomes, lipoproteins, films, plastics,lipophilic microspheres or similar materials.

In certain embodiments, the carrier molecule comprises a specificbinding pair member wherein the pH-sensitive fluorescent dye compoundsprovided herein are conjugated to a specific binding pair member andused to the formation of the bound pair. Alternatively, the presence ofthe labeled specific binding pair member indicates the location of thecomplementary member of that specific binding pair; each specificbinding pair member having an area on the surface or in a cavity whichspecifically binds to, and is complementary with, a particular spatialand polar organization of the other. In this instance, the dye compoundsdisclosed herein function as a reporter molecule for the specificbinding pair. Exemplary binding pairs are set forth in Table 3.

TABLE 3 Representative Specific Binding Pairs Antigen Antibody biotinavidin (or streptavidin or anti-biotin) IgG* protein A or protein G drugdrug receptor folate folate binding protein toxin toxin receptorcarbohydrate lectin or carbohydrate receptor peptide peptide receptorprotein protein receptor enzyme substrate enzyme DNA (RNA) cDNA(cRNA)^(†) hormone hormone receptor ion chelator *IgG is animmunoglobulin ^(†)cDNA and cRNA are the complementary strands used forhybridization

Solid Supports:

In certain embodiments, the pH-sensitive dye compounds disclosed hereinare covalently bonded to a solid support. The solid support may beattached to the dye compounds either through the aniline moiety,fluorophore, or through a reactive group, if present, or through acarrier molecule, if present. Even if a reactive group and/or a carriermolecule are present, the solid support may be attached through theaniline moiety or fluorophore. In certain embodiments, at least onemember selected from R¹, R², R³, R⁴, R⁵, and R⁶ is a solid support.Preferably, at least one of R³, R⁴, R⁵, and R⁶ is a solid support, mostpreferred is at least one of R⁴ or R⁵.

Solid supports suitable for use herein are typically substantiallyinsoluble in liquid phases. Solid supports for use herein are notlimited to a specific type of support. Rather, a large number ofsupports are available and are known to one of ordinary skill in theart. Thus, useful solid supports include solid and semi-solid matrixes,such as aerogels and hydrogels, resins, beads, biochips (including thinfilm coated biochips), microfluidic chip, a silicon chip, multi-wellplates (also referred to as microtitre plates or microplates),membranes, conducting and nonconducting metals, glass (includingmicroscope slides) and magnetic supports. More specific examples ofuseful solid supports include silica gels, polymeric membranes,particles, derivatized plastic films, glass beads, cotton, plasticbeads, alumina gels, polysaccharides such as Sepharose®, poly(acrylate),polystyrene, poly(acrylamide), polyol, agarose, agar, cellulose,dextran, starch, FICOLL®, heparin, glycogen, amylopectin, mannan,inulin, nitrocellulose, diazocellulose, polyvinylchloride,polypropylene, polyethylene (including poly(ethylene glycol)), nylon,latex bead, magnetic bead, paramagnetic bead, superparamagnetic bead,starch and the like.

In certain embodiments, the solid support may include a solid supportreactive functional group, including, but not limited to, hydroxyl,carboxyl, amino, thiol, aldehyde, halogen, nitro, cyano, amido, urea,carbonate, carbamate, isocyanate, sulfone, sulfonate, sulfonamide,sulfoxide, etc., for attaching the dye compounds disclosed herein.Useful reactive groups are disclosed above and are equally applicable tothe solid support reactive functional groups herein.

A suitable solid phase support may be selected on the basis of desiredend use and suitability for various synthetic protocols. For example,where amide bond formation is desirable to attach the pH-sensitivefluorescent dye compounds disclosed herein to the solid support, resinsgenerally useful in peptide synthesis may be employed, such aspolystyrene (e.g., PAM-resin obtained from Bachem Inc., PeninsulaLaboratories, etc.), POLYHIPE™ resin (obtained from Aminotech, Canada),polyamide resin (obtained from Peninsula Laboratories), polystyreneresin grafted with polyethylene glycol (TentaGel™, Rapp Polymere,Tubingen, Germany), polydimethyl-acrylamide resin (available fromMilligen/Biosearch, California), or PEGA beads (obtained from PolymerLaboratories).

Preparation of Conjugates:

In certain embodiments, conjugates of the pH-sensitive fluorescent dyecompounds disclosed herein are provided. Conjugates of components(carrier molecules or solid supports), e.g., drugs, peptides, toxins,nucleotides, phospholipids, proteins and other organic molecules areprepared by organic synthesis methods using the pH-sensitive fluorescentdye compounds disclosed herein, are generally prepared by means wellrecognized in the art (Haugland, MOLECULAR PROBES HANDBOOK, supra,(2002)). Preferably, conjugation to form a covalent bond consists ofmixing the pH-sensitive fluorescent dye compounds disclosed herein in asuitable solvent in which both the pH-sensitive fluorescent dye compoundand the substance to be conjugated are soluble. The reaction preferablyproceeds spontaneously without added reagents at room temperature orbelow. For those reactive compounds that are photoactivated, conjugationis facilitated by illumination of the reaction mixture to activate thereactive compound. Chemical modification of water-insoluble substances,so that a desired compound-conjugate may be prepared, is preferablyperformed in an aprotic solvent such as dimethylformamide,dimethylsulfoxide, acetone, ethyl acetate, toluene, or chloroform.Similar modification of water-soluble materials is readily accomplishedthrough the use of the instant reactive compounds to make them morereadily soluble in organic solvents.

Preparation of peptide or protein conjugates typically comprises firstdissolving the protein to be conjugated in aqueous buffer at about 1-10mg/mL at room temperature or below. Bicarbonate buffers (pH about 8.3)are especially suitable for reaction with succinimidyl esters, phosphatebuffers (pH about 7.2-8) for reaction with thiol-reactive functionalgroups and carbonate or borate buffers (pH about 9) for reaction withisothiocyanates and dichlorotriazines. The appropriate reactive compoundis then dissolved in a nonhydroxylic solvent (usually DMSO or DMF) in anamount sufficient to give a suitable degree of conjugation when added toa solution of the protein to be conjugated. The appropriate amount ofcompound for any protein or other component is convenientlypredetermined by experimentation in which variable amounts of the dyecompound are added to the protein, the conjugate is chromatographicallypurified to separate unconjugated dye compound and the dyecompound-protein conjugate is tested in its desired application.

Following addition of the pH-sensitive fluorescent dye compound to thecomponent solution, the mixture is incubated for a suitable period(typically about 1 hour at room temperature to several hours on ice),the excess pH-sensitive fluorescent dye compound is removed by gelfiltration, dialysis, HPLC, adsorption on an ion exchange or hydrophobicpolymer or other suitable means. The pH-sensitive fluorescent dyecompound-conjugate may be used in solution or lyophilized. In this way,suitable conjugates may be prepared from antibodies, antibody fragments,avidins, lectins, enzymes, proteins A and G, cellular proteins,albumins, histones, growth factors, hormones, and other proteins.

Conjugates of polymers, including biopolymers and other higher molecularweight polymers are typically prepared by means well recognized in theart (for example, Brinkley et al., Bioconjugate Chem., 3:2 (1992)). Inthese embodiments, a single type of reactive site may be available, asis typical for polysaccharides) or multiple types of reactive sites(e.g. amines, thiols, alcohols, phenols) may be available, as is typicalfor proteins. Selectivity of labeling is best obtained by selection ofan appropriate reactive dye compound. For example, modification ofthiols with a thiol-selective reagent such as a haloacetamide ormaleimide, or modification of amines with an amine-reactive reagent suchas an activated ester, acyl azide, isothiocyanate or3,5-dichloro-2,4,6-triazine. Partial selectivity may also be obtained bycareful control of the reaction conditions.

When modifying polymers with the pH-sensitive fluorescent dye compoundsdisclosed herein, an excess of pH-sensitive fluorescent dye compound istypically used, relative to the expected degree of pH-sensitivefluorescent dye compound substitution. Any residual, unreactedpH-sensitive fluorescent dye compound or a pH-sensitive fluorescent dyecompound hydrolysis product is typically removed by dialysis,chromatography or precipitation. Presence of residual, unconjugated dyemay be detected by thin layer chromatography using a solvent that elutesthe dye away from its conjugate. In all cases it is usually preferredthat the reagents be kept as concentrated as practical so as to obtainadequate rates of conjugation.

In certain embodiments, the dye-conjugates disclosed herein areassociated with an additional substance, that binds either to thefluorophore or the conjugated substance (carrier molecule or solidsupport) through noncovalent interaction. In another exemplaryembodiment, the additional substance is an antibody, an enzyme, ahapten, a lectin, a receptor, an oligonucleotide, a nucleic acid, aliposome, or a polymer. The additional substance is optionally used toprobe for the location of the dye-conjugate, for example, as a means ofenhancing the signal of the dye-conjugate.

In certain embodiments, compositions are provided for determining the pHof a sample, the compositions comprising:

a) one or more of the pH-sensitive fluorescent dye compounds describedherein; and

b) a carrier,

wherein the one or more of the pH-sensitive fluorescent dye compoundsare present in an amount effective to detect the pH of the sample.

In certain embodiments, compositions are provided for determining the pHof a sample, the compositions comprising:

(a) one or more of the pH-sensitive fluorescent dye compounds describedherein; and

(b) an analyte,

wherein the one or more of the pH-sensitive fluorescent dye compoundsare present in an amount effective to detect the pH of the sample.

In certain embodiments, the analyte is a cell and the pH-sensitivefluorescent dye compound is located inside the cell. In certainembodiments, the analyte is a protein, lipid or nucleic acid. In certainembodiments, the pH-sensitive fluorescent dye compound is conjugated toa carrier molecule.

Methods:

In certain embodiments, the pH-sensitive fluorescent dye compounds,dye-conjugates and compositions provided herein may be used in methodsincluding, but not limited to, methods to determine the pH of livingcells or cell compartments, to determine a change in pH to the localenvironment caused by a cell, and directly and indirectly detectspecific cellular events associated with a change in pH. In certainembodiments, the methods involve detecting contamination in cell cultureor on agar plates. For the sake of clarity, the sample may also includematerial other than live cells and cell compartments such as, but notlimited to, cell culture medium, biological fluids, diagnosticmaterials, and bacterial medium such as agar plates. As used herein, theterm “a cell compartment” refers to one of the many organelles suspendedin the cell cytoplasm. The pH of a cell or cell compartment may bemeasured by introducing one or more of the pH-sensitive fluorescent dyecompounds, dye conjugates or compositions provided herein into a cell orcell compartment, irradiating the dye or dye conjugate with a suitablelight source, and observing the intensity of fluorescence of the dye orconjugate. The observed fluorescence intensity may then be used todetermine pH by a variety of methods known in the field, selectedaccording to the method of accumulation of the dye compound or dyeconjugate. For instance, the observed fluorescence may be compared to aknown standard, for example a calibration curve of fluorescenceintensity versus pH, or to fluorescence intensity measurementsindicative of the total pH-sensitive fluorescent dye compound, dyeconjugate, or composition present. Any conventional fluorimetricequipment may be used to irradiate the sample, and to measure theresulting fluorescent response.

As stated above the sample may comprise live cells, intracellularfluids, extracellular fluids, biological fluids, sera, biologicalfermentation media, environmental sample, industrial samples, proteins,peptides, buffer solutions, biological fluids or chemical reactors,blood cells, immune cells, cultured cells, muscle tissue, neurons,extracellular vesicles; vascular tissue, blood fluids, saliva, urine,water, soil, waste water, sea water; pharmaceuticals, foodstuffs orbeverages. In certain embodiments, the sample is immobilized on apolymeric membrane, within a polymeric gel, on a microparticle, on amicroarray, on a silicon chip, on a glass slide, on a microwell plate,and on a microfluidic chip.

The pH-sensitive fluorescent dye compounds disclosed herein maytherefore be used as pH sensors in relation to samples comprising orsuspected of comprising a biological entity or biological substance. ThepH-sensitive fluorescent dye compounds disclosed herein may be used inassays involving a biological entity or biological substance. In certainembodiments, the invention provides for the use of the pH-sensitivefluorescent dye compounds in a biological assay for the purposesdescribed herein, particularly as a pH sensor.

Thus, in certain embodiments, the methods disclosed herein comprisedetermining the pH of a sample, wherein the methods comprise:

(a) contacting the sample with one or more of the pH-sensitivefluorescent dye compounds disclosed herein, to form a contacted sample;

(b) incubating the contacted sample for an appropriate amount of time toform an incubated sample;

(c) illuminating the incubated sample with an appropriate wavelength toform an illuminated sample; and

(d) detecting fluorescent emissions from the illuminated sample;

wherein the fluorescent emissions are used to determine the pH of thesample.

In certain embodiments, the methods disclosed herein comprisedetermining the pH of a sample, wherein the methods comprise:

(a) contacting the sample with one or more of the compositions providedherein to form a contacted sample;

(b) incubating the contacted sample for an appropriate amount of time toform an incubated sample;

(c) illuminating the incubated sample with an appropriate wavelength toform an illuminated sample; and

(d) detecting fluorescent emissions from the illuminated sample;

wherein the fluorescent emissions are used to determine the pH of thesample.

In certain embodiments, the pH-sensitive fluorescent dye compoundsdisclosed herein are used in cell culture for detection ofcontamination. In certain embodiments, the pH-sensitive fluorescent dyecompounds disclosed herein are used in or on agar plates for thedetection of contamination.

In certain embodiments, a change in the pH inside the cell correspondsto a cellular process. In certain embodiments, the pH-sensitivefluorescent dye compound is conjugated to a protein, nucleic acid orlipid. In certain embodiments, the pH-sensitive fluorescent dye compoundis conjugated to transferrin. In certain embodiments, the pH-sensitivefluorescent dye compound is conjugated to a carrier molecule through asuccinimidyl ester. In certain embodiments the pH-sensitive fluorescentdye compound is conjugated to epithelial growth factor (EGF) or EGFreceptor (EGFR). In certain embodiments the pH-sensitive fluorescent dyecompound is non-fluorescent before entering the cell. More particularly,the pH-sensitive fluorescent dye compound becomes fluorescent afterentering the cell. In certain embodiments, the pH-sensitive fluorescentdye compound enters the cell through phagocytosis. In certainembodiments, the pH-sensitive fluorescent dye compound enters the cellthrough receptor-mediated endocytosis.

In certain embodiments, methods are provided for monitoring the pHinside a live cell, the methods comprising:

(a) contacting the cell with a pH-sensitive fluorescent dye compounddisclosed herein to form a contacted cell;

(b) incubating the contacted cell for a sufficient amount of time forthe one or more pH-sensitive fluorescent dye compounds to enter the cellto form a labeled cell;

(c) illuminating the labeled cell with an appropriate wavelength to forman illuminated cell; and

(d) detecting fluorescent emissions from the illuminated cell;

wherein the fluorescent emissions are used to monitor the pH inside thecell.

In certain embodiments, methods are provided for monitoring the pHinside a live cell, the methods comprising:

(a) contacting the cell with one or more of the compositions providedherein to form a contacted cell;

(b) incubating the contacted cell for a sufficient amount of time forthe one or more compositions to enter the cell to form a labeled cell;

(c) illuminating the labeled cell with an appropriate wavelength to forman illuminated cell; and

(d) detecting fluorescent emissions from the illuminated cell;

wherein the fluorescent emissions are used to monitor the pH inside thecell.

Typically, the pH-sensitive fluorescent dyes and/or dye conjugatesand/or compositions disclosed herein are introduced into a living cellor cell compartment by mixing with a sample comprising a cell or cellcompartment, and then leaving the mixture to incubate for a timeinterval adequate to allow entry of the pH-sensitive fluorescent dye,dye conjugate, or composition into the cell or cell compartment. Duringthis time interval, the pH-sensitive fluorescent dye compound, dyeconjugate, or composition either passively diffuses across the plasmamembrane or is taken up by the cell or cell compartment by a cellmediated mechanism.

In the case of conjugates, typically target molecules, includingbacterial particles that induce phagocytosis and specific bindingproteins that bind a cellular receptor and induce receptorinternalization, are generally cell or cell compartment specific, hencea specific conjugate generally attaches to only one kind of cell or cellcompartment. Once attached to a cell or cell compartment, thepH-sensitive fluorescent dye conjugate may diffuse through a membrane ofthat cell or cell compartment or be trafficked to a specific cellcompartment by receptor-mediated endocytosis, hence exposing itself tothe internal pH of the cell or cell compartment.

Advantageously, the pH-sensitive fluorescent dye compounds, dyeconjugates, and compositions disclosed herein allow for a more accuratedetermination of pH as compared to existing pH sensor dyes because thepKa's of the pH-sensitive fluorescent dye compounds, dye conjugates, andcompositions disclosed herein may, by design, be adjusted bysubstitution to a variety of pKa values. This is accomplished by theaddition of EDG groups on the aniline moiety and by substitution at oneof the remaining R₁-R⁶ with a group that is not —OH or —SH. Thus, someare tuned to the pH of the cell or cell compartment of interest, andconsequently will be ideal for measuring the pH of a cell or cellcompartment when accumulated by receptor-mediated endocytosis or anynon-passive accumulation mechanism as well as by passive accumulation.Others will have a pKa far from the pH of the cell media orextracellular matrix. The pH-sensitive fluorescent dye compoundsdisclosed herein are tuned to match the sample of choice with theunderstanding that the dye compounds become fluorescent when the pH ofthe sample drops below the pKa of the pH-sensitive fluorescent dyecompound(s) disclosed herein. In certain embodiments, the pKa of thepH-sensitive fluorescent dye compound may be modified by the addition ofa dialkylamino group at position R³ advantageously resulting in aphysiological pKa. In certain embodiments, the dialkylamino group isdiethylamino. In certain embodiments, the dialkylamino group isdimethylamino.

Accumulation will occur passively when one form of the pH-sensitivefluorescent dye compound, dye conjugate, or composition with respect topH (the uncharged form) freely penetrates the cell or cell compartmentof interest and the other form (a charged form) is non-penetrating.Fluorescence will approach its equilibrium position provided the form ofthe accumulated dye is the fluorescent form and that accumulation toequilibrium has occurred. The observed fluorescence intensity may thenbe used to determine pH according to any of the known methods, forinstance by reference to calibration data, or by comparing the observedfluorescence intensity to the fluorescence intensity observed onacidifying the test sample so that all the dye or conjugate fluoresces,the ratio of the two fluorescence intensities coupled with the known pKaallowing determination of pH. Passive accumulation may be achieved byuse of a pH-sensitive fluorescent dye compound that is not attached to acarrier molecule or solid support or a pH-sensitive fluorescent dyecompound that is attached to a small, relatively hydrophobic targetmolecule capable of diffusing through the cell membrane, such as one ormore acetoxymethoxy (AM) ester groups. However, we have found thatpH-sensitive fluorescent dye compounds comprising a reactive group, suchas succinimidyl ester, also appear to passively accumulate in cells.

In certain embodiments, methods are provided for identifying a targetcell within a population of cells wherein the target cell isdifferentially labeled relative to neighboring cells within thepopulation, the methods comprising:

(a) contacting one or more of the pH-sensitive fluorescent dye compoundsdisclosed herein with the population of cells to form a contacted cellpopulation;

(b) incubating the contacted cell population for a period of timesufficient for the one or more pH-sensitive fluorescent dye compounds toenter the target cell, thereby forming an incubated cell population; and

(c) illuminating the incubated cell population, wherein the target cellis identified by a differential label relative to neighboring cellswithin the population.

In certain embodiments, methods are provided for identifying a targetcell within a population of cells wherein the target cell isdifferentially labeled relative to neighboring cells within thepopulation, the methods comprising:

(a) contacting one or more of the compositions disclosed herein with thepopulation of cells to form a contacted cell population;

(b) incubating the contacted cell population for a period of timesufficient for the one or more compositions to enter the target cell,thereby forming an incubated cell population; and

(c) illuminating the incubated cell population, wherein the target cellis identified by a differential label relative to neighboring cellswithin the population.

In certain embodiments, the target cell is a neuronal cell. In certainembodiments, the neuronal cell is identified by increased fluorescenceas compared with neighboring cells. In certain embodiments, thepopulation of cells is part of a tissue. More particularly, the tissueis selected from the group consisting of tumor tissue, epidermal tissue,muscle tissue, bone marrow tissue, neural tissue, brain tissue, organtissue, and human biopsy tissue.

In certain embodiments, methods are provided for identifying a firstneuron or plurality of neurons in a neural tissue slice, or a neuronalcell is a heterogeneous mixture comprising neuronal and non-neuronalcell types. Also provided are methods for detecting the effect of aneuromodulator on a connection between neurons or a plurality of neuronsforming a circuit; methods for identifying an inhibitory connectionbetween or on neurons; and methods for identifying neurons in vivo or invitro.

In certain embodiments, healthy neurons are identified in mixed culturesof living cells or preparations of cells, such as tissue slices or wholemount. In vivo identification of neurons or other metabolically activecells such as cardiac and skeletal myocytes are particularly preferredmethods employing the pH-sensitive dye compounds disclosed herein.

Non-passive accumulation may occur through cell-mediated mechanisms suchas phagocytosis and endocytosis, typically when a pH-sensitivefluorescent dye compound disclosed herein comprises a carrier moleculeor solid support that is bound by a cellular receptor. In this instance,whenever the dye compound provided herein is accumulated in the cell orcell compartment by a mechanism that does not rely solely on passiveaccumulation, the accuracy of a pH measurement will be highest when thepKa of the dye compound is near the pH to be measured. In thissituation, without wishing to be bound by a theory, the increasedaccuracy available with the pH-sensitive dye compounds disclosed hereinmay arise from the fact that the pKa is the pH of the aqueous mediumcontaining a species when it is 50% protonated and that at this pH achange in proton intensity will have greatest effect on the propertiesof the species. Hence, the greatest change in fluorescence intensityoccurs at the pKa of the pH-sensitive fluorescent dye, and measurementsof absolute fluorescence intensity at this pH so that the pH-sensitivefluorescent dye compounds used to analyze a particular cell or cellcompartment embraces the pH of that cell or cell compartment isgenerally sufficient.

In certain embodiments, methods are provided for detecting a pH relatedintracellular process, the methods comprising:

(a) contacting one or more of the pH-sensitive fluorescent dye compoundsdisclosed herein with a cell to form a contacted cell;

(b) incubating the contacted cell to form an incubated solution;

(c) illuminating the incubated solution to form an illuminated solution;and

(d) detecting fluorescent emissions from the illuminated solution;

wherein increased fluorescent emissions indicates activation of theintracellular process.

In certain embodiments, methods are provided for detecting a pH relatedintracellular process, the methods comprising:

(a) contacting one or more of the compositions provided herein with acell to form a contacted cell;

(b) incubating the contacted cell to form an incubated solution;

(c) illuminating the incubated solution to form an illuminated solution;and

(d) detecting fluorescent emissions from the illuminated solution;

wherein increased fluorescent emissions indicates activation of theintracellular process.

In certain embodiments, the intracellular process is the opening of anion channel. More particular still, the ion channel is calcium.

In certain embodiments, the pH-sensitive fluorescent dye compound isinternalized after incubation with the cytosol of the cell.

Certain embodiments provide for a no-wash, no-quench assay forphagocytosis that is based on fluorogenic bioparticles comprising thepH-sensitive fluorescent dye compounds provided herein. Currentprotocols for measuring phagocytosis that use fluorescent bioparticles,require a trypan blue quenching step and several washing steps. Thesesteps can introduce significant variability in the assay. To addressthis issue, provided herein is a no-wash phagocytosis kit, using E. colibioparticles conjugated to a pH-sensitive fluorescent dye as describedherein. These bioparticle conjugates are weakly fluorescent atextracellular pH. However, when added to phagocytic J774.2 murinemacrophages, they become ingested into acidic compartments and fluorescefrom within the cells, giving specific signals that meet or exceed thebrightness of the Vybrant™ Phagocytosis Assay Kit (Life TechnologiesCorporation). Quantitation of the phagocytic index with these conjugatesrequires no wash or quenching steps, and uptake of the bioparticles ispotently inhibited by cytochalaisin D, a known blocker of phagocytosis.The pH-sensitive fluorescent bioparticles described herein may be usedin plate based, as well as imaging and flow cytometry assays ofphagocytosis.

In certain embodiments, methods are provided for detecting phagocytosisof a carrier molecule in solution, the methods comprising:

(a) conjugating the carrier molecule to one or more of the pH-sensitivefluorescent dye compounds disclosed herein to form a carrier-dyeconjugate;

(b) contacting the carrier-dye conjugate with a cell to form a contactedcell;

(c) incubating the contacted cell to form an incubated solution;

(d) illuminating the incubated solution to form an illuminated solution;and

(e) detecting fluorescent emissions from the illuminated solution;

wherein fluorescent emissions indicate phagocytosis of the carriermolecule.

In certain embodiments, methods are provided for detecting phagocytosisof a carrier molecule in solution, the methods comprising:

(a) conjugating the carrier molecule to one or more of the compositionsdisclosed herein to form a carrier-dye conjugate;

(b) contacting the carrier-dye conjugate with a cell to form a contactedcell;

(c) incubating the contacted cell to form an incubated solution;

(d) illuminating the incubated solution to form an illuminated solution;and

(e) detecting fluorescent emissions from the illuminated solution;

wherein fluorescent emissions indicate phagocytosis of the carriermolecule.

In certain embodiments, the carrier molecule is an E. coli bioparticle.

In certain embodiments, methods are provided for diagnosing or detectinga disease in a subject, the methods comprising:

(a) contacting a sample obtained from a subject suspected of having thedisease with one or more of the pH-sensitive fluorescent dye compoundsdisclosed herein, to form a contacted sample;

(b) incubating the contacted sample for an appropriate amount of time toform an incubated sample;

(c) illuminating the incubated sample with an appropriate wavelength toform an illuminated sample; and

(d) detecting fluorescent emissions from the illuminated sample;

wherein the fluorescent emissions are used to diagnose or detect thedisease.

In certain embodiments, methods are provided for diagnosing or detectinga disease in a subject, the methods comprising:

(a) contacting a sample obtained from a subject suspected of having thedisease with one or more of the compositions disclosed herein, to form acontacted sample;

(b) incubating the contacted sample for an appropriate amount of time toform an incubated sample;

(c) illuminating the incubated sample with an appropriate wavelength toform an illuminated sample; and

(d) detecting fluorescent emissions from the illuminated sample;

wherein the fluorescent emissions are used to diagnose or detect thedisease.

In certain embodiments, the disease is associated with the centralnervous system. In certain embodiments, the disease is Alzheimer'sdisease (AD). In certain embodiments, the pH-sensitive fluorescent dyecompound is conjugated to a carrier molecule associated with thedisease. In certain embodiments, the pH-sensitive fluorescent dyecompound is conjugated to β-amyloid or a fragment or thereof.Accordingly, certain embodiments provide a blood based assay forAlzheimer's disease, based on the phagocytosis of the pH-sensitivefluorescent dye compounds disclosed herein conjugated to β-amyloidprotein.

In certain embodiments, the disease is associated with the immunesystem. In certain embodiments, the disease is associated withinflammation. In certain embodiments, the disease is cancer. In certainembodiments, the disease is associated with oxidative stress. In certainembodiments, the pH-sensitive fluorescent dye compound is conjugated toa carrier molecule associated with the disease.

In certain embodiments, methods are provided for detecting a targetmolecule capable of modulating a cellular process that affects the pH ordirectly affects the pH of a cell. In certain embodiments, the targetmolecule is a small molecule. In certain embodiments, the cell is aneuronal cell. In certain embodiments, the cell is a cancer cell. Incertain embodiments, the cell is an immune cell.

In certain embodiments, methods are provided for detecting any one ofthe following with a pH-sensitive fluorescent dye compound as describedherein: an antibody, protein, peptide, enzyme substrate, hormone,lymphokine, metabolite, receptor, antigen, hapten, lectin, avidin,streptavidin, toxin, carbohydrate, oligosaccharide, polysaccharide,nucleic acid, derivatized deoxy nucleic acid, DNA fragment, RNAfragment, derivatized DNA fragment, derivatized RNA fragment,nucleoside, nucleotide, natural drug, synthetic drug, virus particle,bacterial particle, virus component, yeast component, blood cell, bloodcell component, plasma component, serum component, biological cell,neuronal cells, noncellular blood component, bacteria, bacterialcomponent, natural or synthetic lipid vesicle, poison, environmentalpollutant, polymer, polymer particle, glass particle, glass surface,plastic particle, plastic surface, polymer membrane, conductor orsemiconductor comprising detecting a compound disclosed herein bound tosaid antibody, protein, peptide, enzyme substrate, hormone, lymphokine,metabolite, receptor, antigen, hapten, lectin, avidin, streptavidin,toxin, carbohydrate, oligosaccharide, polysaccharide, nucleic acid,derivatized deoxy nucleic acid, DNA fragment, RNA fragment, derivatizedDNA fragment, derivatized RNA fragment, nucleoside, nucleotide, naturaldrug, synthetic drug, virus particle, bacterial particle, viruscomponent, yeast component, blood cell, blood cell component, plasmacomponent, serum component, biological cell, noncellular bloodcomponent, bacteria, bacterial component, natural or synthetic lipidvesicle, poison, environmental pollutant, polymer, polymer particle,glass particle, glass surface, plastic particle, plastic surface,polymer membrane, conductor or semiconductor.

In certain embodiments, methods are provided for detecting acidic orbasic conditions comprising contacting a pH-sensitive fluorescent dyecompound as described herein with a composition suspected of beingacidic or basic and detecting the fluorescence of the pH-sensitivefluorescent dye compound as an indicator of said acidic or basicconditions. In certain embodiments, the composition being testedcomprises an intracellular environment.

Accuracy for the general means of measuring pH may be further increasedby using a plurality of the pH-sensitive fluorescent dye compoundsprovided herein having different fluorescent responses. In certainembodiments, two or more pH-sensitive fluorescent dye compoundsaccording to the present invention may be used, optionally bonded toidentical carrier molecules or solid supports, or a pH-sensitivefluorescent dye compound as disclosed herein and another different dye.In certain embodiments, the second fluorescent dye has a positivefluorescence response with increasing pH (i.e., that the intensity offluorescence exhibited by the dye or complex increases with increasingpH). It is preferable that the two or more dyes have overlappingtitration ranges, and more preferably the different dyes or conjugateshave pKa values within about 1 unit of each other. The intensity of thefluorescence of each dye compound or dye-conjugate is then measured, andpH determined by calculating the ratio of the fluorescence intensity ofthe first compound to the fluorescence intensity of the second compoundand then comparing the value obtained to a calibration curve.

In certain embodiments, the pH-sensitive dye compounds may be used toanalyze the kinetics of migration of a species into or through a cell orcell compartment. This may be done by monitoring the fluorescenceintensity of a pH-sensitive dye compound over a time interval. Where pHis known, the pH-sensitive dye compound should be selected so as to havea pKa in the range between the pH at the starting point and the pH atthe end point of the pathway to be analyzed. In some cases it may bedesirable to use a plurality of pH-sensitive dye compounds having avariety of pKa values, with each dye or complex tuned to a differentportion of the pathway to be analyzed.

In certain embodiments, methods are provided for using a pH-sensitivefluorescent dye compound, dye conjugate, or composition provided hereinfor analysis or detection. More particularly, the detection may beperformed by optical means. In certain embodiments, the fluorescenceemission is optionally detected by visual inspection, or by use of anyof the following devices: CCD cameras, video cameras, photographic film,laser scanning devices, fluorometers, photodiodes, quantum counters,epifluorescence microscopes, scanning microscopes, flow cytometers,fluorescence microplate readers, or by means for amplifying the signalsuch as photomultiplier tubes.

In certain embodiments, the sample or medium in which a pH-sensitivefluorescent dye compound provided herein is present is illuminated witha wavelength of light selected to give a detectable optical response,and observed with a means for detecting the optical response. Equipmentthat is useful for illuminating the pH-sensitive fluorescent dyecompounds and compositions disclosed herein includes, but is not limitedto, hand-held ultraviolet lamps, mercury arc lamps, xenon lamps, lasersand laser diodes. These illumination sources are optically integratedinto laser scanners, fluorescence microplate readers or standard ormicrofluorometers.

The pH-sensitive fluorescent dye compounds, dye conjugates, andcompositions disclosed herein may, at any time after or during an assay,be illuminated with a wavelength of light that results in a detectableoptical response, and observed with a means for detecting the opticalresponse. Upon illumination, such as by an ultraviolet or visiblewavelength emission lamp, an arc lamp, a laser, or even sunlight orordinary room light, the fluorescent compounds, including those bound tothe complementary specific binding pair member, display intense visibleabsorption as well as fluorescence emission. Selected equipment that isuseful for illuminating the fluorescent pH-sensitive fluorescent dyecompounds disclosed herein include, but is not limited to, hand-heldultraviolet lamps, mercury arc lamps, xenon lamps, argon lasers, laserdiodes, and YAG lasers. These illumination sources are optionallyintegrated into laser scanners, fluorescence microplate readers,standard or mini fluorometers, or chromatographic detectors. Thisfluorescence emission is optionally detected by visual inspection, or byuse of any of the following devices: CCD cameras, video cameras,photographic film, laser scanning devices, fluorometers, photodiodes,quantum counters, epifluorescence microscopes, scanning microscopes,flow cytometers, fluorescence microplate readers, or by means foramplifying the signal such as photomultiplier tubes. Where the sample isexamined using a flow cytometer, a fluorescence microscope or afluorometer, the instrument is optionally used to distinguish anddiscriminate between the fluorescent compounds disclosed herein and asecond fluorophore with detectably different optical properties,typically by distinguishing the fluorescence response of the fluorescentcompounds of the invention from that of the second fluorophore. Where asample is examined using a flow cytometer, examination of the sampleoptionally includes isolation of particles within the sample based onthe fluorescence response by using a sorting device. In certainembodiments, the illumination source is used to form a covalent bondbetween the present pH-sensitive fluorescent dye compound and an analyteof interest. In this instance the pH-sensitive fluorescent dye comprisesa photoactivatable reactive group, such as those discussed above.

Kits:

In certain embodiments, kits are provided for determining the pH of asample comprising:

(a) one or more of the pH-sensitive fluorescent dye compounds describedherein;

(b) one or more containers; and optionally

(c) instructions for determining the pH of the sample.

In certain embodiments, kits are provided for determining the pH of asample comprising:

(a) one or more of the pH-sensitive fluorescent dye compositionsdescribed herein;

(b) one or more containers; and optionally

(c) instructions for determining the pH of the sample.

In certain embodiments, the kits further comprise one or more of thefollowing: a buffering agent, a purification medium, a vial comprisingthe sample, or an organic solvent.

As used herein, the term “kit” refers to a packaged set of relatedcomponents, typically one or more pH-sensitive fluorescent dye compoundsor compositions. In certain embodiments, the kits disclosed hereincomprise one or more of the pH-sensitive fluorescent dye compoundsdescribed herein, one or more carriers suitable for in vitro or in vivoapplications, and one or more containers in which to store the one ormore pH-sensitive fluorescent dyes and/or one or more carriers, such assolvents, buffers, stabilizers, pH adjusting agents, etc. The kitoptionally contains instructions for how to prepare the one or morepH-sensitive fluorescent dyes or how to prepare a composition containingthe one or more pH-sensitive fluorescent dye, and how to administer thedye or composition containing the dye. In certain embodiments, the kitcomprises instructions for performing an assay that detects the pH or pHchanges in samples. In certain embodiments, the assay is an in vitroassay. In certain embodiments, the assay is an in vivo assay. The kitmay further comprise one or more pieces of equipment to administer thedye compound, or composition containing the pH-sensitive fluorescent dyecompound including, but not limited to, syringes, pipettes, pipettebulbs, spatulas, vials, syringe needles, and various combinationsthereof.

In certain embodiments, the kits provided herein comprise indicatorsolutions or indicator “dipsticks”, blotters, culture media, cuvettes,and the like. In certain embodiments, the kits provided herein compriseindicator cartridges (where a kit component is bound to a solid support)for use in an automated detector. In certain embodiments, the kitsprovided herein further comprise molecular weight markers, wherein saidmarkers are selected from phosphorylated and non-phosphorylatedpolypeptides, calcium-binding and non-calcium binding polypeptides,sulfonated and non-sulfonated polypeptides, and sialylated andnon-sialylated polypeptides. In certain embodiments, the kits providedherein further comprise a member selected from a fixing solution, adetection reagent, a standard, a wash solution, and combinationsthereof.

Synthesis and Processes of Preparation of the pH-Sensitive FluorescentDye Compounds:

In certain embodiments processes are provided for synthesizing acompound of structural formula (I):

the process comprising:

-   -   a) contacting a compound of structural formula (VI):

-   -   with a compound of structural formula (IV):

-   -   to form a compound of structural formula (VII):

-   -   b) de-allylating the compound of structural formula (VII), when        R⁷, R⁸, R⁹ and R₁₀ are each allyll, to form a compound of        structural formula (I),

wherein R¹, R², R³, R⁴, R⁵, R⁶ are as previously defined herein.

In certain embodiments, processes are provided for synthesizing acompound of structural formula (II):

the process comprising:

-   -   a) contacting a compound of structural formula (III):

-   -   with a compound of structural formula (IV):

-   -   to form a compound of structural formula (V):

b) de-allylating the compound of structural formula (V), when R⁷ and R⁸are each allyl, to form a compound of structural formula (II), andwherein R¹, R², R³, R⁴, R⁵ and R⁶ are as previously defined herein.

An exemplary reaction scheme is shown in detail below:

wherein R¹, R², R³, R⁴, R⁵, R⁶, R⁷ and R⁸ are as previously definedherein.

In one illustrative embodiment of such a process, a compound ofstructural formula (I) is prepared in Scheme 3:

In another illustrative embodiment of such a process, a compound ofstructural formula (I) is prepared in Scheme 4:

In yet another illustrative embodiment of such a process, a compound ofstructural formula (II) is prepared in Scheme 5:

In yet another illustrative embodiment of such a process, a compound ofstructural formula (I) is prepared in Scheme 6:

In certain embodiments, any one of the above methods of synthesisfurther comprises a purifying step. In certain more particularembodiments, the purifying step comprises at least one of: columnchromatography, trituration, recrystallization, filtration, or aqueousseparation.

A detailed description of the present teachings having been providedabove, the following examples are given for the purpose of illustratingthe invention and shall not be construed as being a limitation on thescope of the invention or claims.

EXAMPLES

Referring to the examples that follow, pH-sensitive fluorescent dyecompounds disclosed herein were synthesized using the methods describedherein, or other methods, which are known in the art.

It should be understood that the organic compounds according to theinvention may exhibit the phenomenon of tautomerism. As the chemicalstructures within this specification can only represent one of thepossible tautomeric forms, it should be understood that the inventionencompasses any tautomeric form of the drawn structure.

Chemical Synthesis of the Fluorescent pH-sensitive Dye CompoundsDisclosed Herein:

Example 1 Preparation of Compound (5)

Compound (5) can be obtained via multistep synthesis from compound (4),according to U.S. Patent Publication No. 2008/076524, hereinincorporated by reference in its entirety.

Example 2 Preparation of Compounds (7) and (8)

Compound (6) (9.00 g, 18.3 mmol, see Wu et al., Org. Lett. 10:1779-1782(2008), herein incorporated by reference in its entirety) was treatedwith DMSO (56 mL) and diallylamine (21.2 g, 219 mmol) at roomtemperature, and the mixture was heated to 90° C. for 36 hours. Themixture was cooled to room temperature, and quenched by adding water(250 mL). The product was extracted with ethyl acetate (200 mL×3). Thecombined organic layers were washed by water (200 mL×2), brine (300 mL),dried by MgSO₄, and evaporated. The crude product was purified bychromatography on silica gel column (Biotage, SNAP 340 g, 6.5×18 cm,ethyl acetate:hexanes=1:2) to give Compound (7) (3.30 g, 47%, whitesolid), and Compound (8) (1.10 g, 20%, pale yellow solid).

Example 3 Preparation of Compound (9)

Compound (7) (149 mg, 0.386 mmol) was treated with anhydrous DCM (5 mL)and Tf₂O (80 μL, 0.476 mmol), and the mixture was stirred at roomtemperature. After 30 min of stirring, Compound (5) (150 mg, 0.486 mmol)in DCM (2 mL) and DIEA (120 μL, 0.689 mmol) were added. The reaction wasstirred at room temperature for 16 hours. Evaporation gave a crudeproduct. The crude product was purified by chromatography on silica gelcolumn (Biotage, SNAP 25 g, 2.5×8 cm, MeOH:CHCl₃=1:10˜1:4) to giveCompound (9) (200 mg, 62%) as a purple gummy material.

Example 4 Preparation of Compound (1)

Compound (9) (200 mg, 0.239 mmol) was treated with MeOH (5 mL) and NaBH₄(36 mg, 0.956 mmol), and the mixture was stirred at room temperature for30 min. The mixture was evaporated, loaded into a short silica gelcolumn (3×5 cm, ethyl acetate:hexanes=1:4) to remove borane sideproduct. Concentration gave the dihydro-form of Compound (9). Thisintermediate was treated with Pd(PPh₃)₄ (30 mg, 0.0259 mmol),1,3-dimethylbarbituric acid (302 mg, 1.93 mmol) and anhydrous DCM (5mL). The new mixture was cooled in dry ice/acetone bath and evacuatedthrough syringe needle. The flask was filled back with argon andevacuation/refilling with argon was repeated two more times. The mixturewas heated to 40° C. for 20 hours under argon atmosphere. DCM wasevacuated by aspirator, and the residue was treated by MeOH (3 mL) andchloranil (120 mg, 0.488 mmol), and the mixture was stirred at roomtemperature for 30 min. MeOH was removed by aspirator, and the crudeproduct was purified by chromatography on silica gel column (Biotage,SNAP 50 g, 3.5×8.5 cm, H₂O:MeCN:HOAc=1:10:0.1˜1:4:0.1) to give Compound(1) (69 mg, 50%) as dark brown gummy material.

Example 5 Preparation of Compound (10)

A solution of Compound (1) (69 mg, 0.121 mmol) in MeOH (10 mL) wastreated with 5 mL of 1 M NaOH, and the mixture was stirred at roomtemperature for 2 hours. 1 M HCl (4.8 mL) was added to quench base. Thewhole mixture was evaporated to give a crude product. The crude productwas purified by chromatography on silica gel column (Biotage SNAP 50 g,MeOH:CHCl₃=1:5˜1:2) to give Compound (10) (30 mg, 51%) as a dark brownsolid.

Example 6 Preparation of Compound (12)

A solution of Compound (10) (20 mg, 0.041 mmol) and DMAP (7.0 mg, 0.057mmol) in DMF (4 mL) was treated with Compound (11) (see U.S. PatentPublication No 2009/0004753, herein incorporated by reference in itsentirety) (24 mg, 0.046 mmol), and the mixture was stirred at roomtemperature for 1 hour. DMF was removed by pump to give a crude product.The product was purified by chromatography on silica gel column (Biotage25 g, 2.5×8 cm, MeOH:CHCl₃=1:3) to give Compound (12) (15 mg, 53%) as abrown solid.

Example 7 Preparation of Compounds (14) and (15)

A solution of 4-methoxyaniline (Compound (13)) (10.0 g, 81.2 mmol) inDMF (100 mL) was treated with 60% NaH (8.10 g, 203 mmol) and iodoethane(26.0 mL, 235 mmol). The temperature of the mixture was kept at 0° C. byice bath in the first 3 hours of stirring. The ice bath was removed andthe mixture was stirred at room temperature for another 12 hours. Water(200 mL) was added to quench this reaction. The product was extracted byethyl acetate (200 mL×3). The combined organic layers were washed bywater (200 mL×5), brine (200 mL), and dried over sodium sulfate.Filtration and evaporation gave Compound (14) (16.2 g, ˜100%) as a darkgreen oil.

To a solution of N,N-diethyl-4-methoxyaniline (Compound (14)) (6.0 g, 27mmol) in water (500 mL) and acetic acid (50 mL) was added a solution ofNaNO₂ (3.8 g, 55 mmol) in water (70 mL) dropwise within 30 min at roomtemperature. The reaction mixture was stirred at room temperature for 3hours. The product was extracted by ethyl acetate (150 mL×3). Thecombined organic layers were washed by 1M KOH (100 mL×4), brine (100 mL)and dried over anhydrous sodium sulfate. Filtration and evaporation gavea crude product as dark red oil. The crude product was purified bychromatography on silica gel column (Biotage, SNAP 100 g, 3.5×16 cm,from 15% CHCl₃ in hexanes to 100% CHCl₃) to give Compound (15) (4.90 g,81%) as a dark red oil.

Example 8 Preparation of Compounds (16) and (17)

To palladium on activated charcoal (650 mg) was added ethanol (15 mL)under argon carefully. A solution of Compound (15) (5.30 g, 23.6 mmol)in ethanol (75 mL) was treated with the palladium suspension solution bya pipet. The solution was equipped with a 3-way stopcock attached by a˜3 L balloon filled with hydrogen. The solution was evacuated andrefilled with hydrogen carefully three times. The solution was stirredunder hydrogen atmosphere for 18 hours. Filtration through a Celite padwas performed to remove palladium, and the filtrate was concentrated todryness to get a crude product. The crude product was purified bychromatography on silica gel column (Biotage, SNAP 100 g, 3.5×16 cm,ethyl acetate:hexanes=1:4) to give Compound (16) (4.14 g, 90%, as lightbrown oil).

A solution of Compound (16) (4.14 g, 21.3 mmol) in DCM (60 mL) wastreated with acetyl chloride (1.80 mL, 25.6 mmol) and triethylamine(4.44 mL, 32.0 mmol) at 0° C. The mixture was stirred at 0° C. for 30min, and quenched by adding MeOH (1 mL). The mixture was diluted byethyl acetate (300 mL) and the solution was washed by water (200 mL),brine (150 mL), and dried over anhydrous sodium sulfate. Evaporationgave pure crude product of Compound (17) (4.73 g, 94%) as a light brownoil. No further purification was required.

Example 9 Preparation of Compounds (18) and (19)

A solution of Compound (17) (4.73 g, 20.0 mmol) in anhydrous THF (15 mL)was treated with BH₃-THF (60 mL of 1M solution in THF, 60 mmol)carefully. The mixture was heated to reflux for 2 hours and cooled toroom temperature. MeOH (60 mL) was added to the solution slowly toquench extra amount of borane complex at room temperature, and themixture was heated to reflux for 10 min. The solution was cooled to roomtemperature, and evaporated to dryness. The residue was dissolved in 300mL of ethyl acetate, and washed by saturated sodium bicarbonate (150mL×2), brine (100 mL), and dried over anhydrous sodium sulfate.Evaporation gave pure crude product of Compound (18) (4.12 g, 93%) as alight brown oil. No further purification was required.

A solution of Compound (18) (4.06 g, 18.3 mmol) in 40 mL of DMF wastreated with methyl 4-bromobutanoate (9.23 mL, 73.1 mmol), Nal (1.36 g,9.07 mmol), and DIEA (9.44 mL, 54.2 mmol), and the mixture was heated to100° C. for 22 hours. The reaction was cooled to room temperature, added200 mL of water, and extracted by ethyl acetate (150 mL×3). The combinedorganic layers were washed by water (150 mL×3), brine (100 mL), driedover anhydrous sodium sulfate, and evaporated to give a crude product.The crude product was purified by chromatography on silica gel column(Biotage, SNAP 100 g, 3.5×16 cm, ethyl acetate:hexanes=1:4) to giveCompound (19) (4.60 g, 79%) as light brown oil.

Example 10 Preparation of Compound (20)

Compound (7) (2.15 g, 5.54 mmol) was treated with anhydrous DCM (50 mL)and Tf₂O (0.94 mL, 0.5.60 mmol), and the mixture was stirred at roomtemperature. After 30 min of stirring, Compound (19) (2.13 g, 6.65 mmol)in DCM (15 mL) and DIEA (1.25 mL, 7.18 mmol) were added. The reactionwas stirred at room temperature for 22 hours. Evaporation gave a crudeproduct. The crude product was purified by chromatography on silica gelcolumn (Biotage, SNAP 100 g, 3.5×16 cm, H₂O:MeCN:HOAc=1:10:0.1˜1:6:0.1)to give Compound (20) (2.58 g, 62%) as a purple gummy material.

Example 11 Preparation of Compound (2)

Compound (20) (2.58 g, 4.27 mmol) was treated with MeOH (20 mL), THF (10mL) and NaBH₄ (330 mg, 8.50 mmol), and the mixture was stirred at roomtemperature for 30 min. The mixture was diluted by 300 mL of ethylacetate, and the combined solution was washed by water (50 mL) and brine(50 mL), and dried over anhydrous sodium sulfate. Concentration gave thedihydro-form of Compound (20). This intermediate was treated withPd(PPh₃)₄ (493 mg, 0.427 mmol), 1,3-dimethylbarbituric acid (3.30 mg,21.0 mmol) and anhydrous DCM (30 mL). The new mixture was cooled in dryice/acetone bath and evacuated through syringe needle. The flask wasfilled back with argon and evacuation/refilling with argon was repeatedtwo more times. The mixture was heated to 40° C. for 20 hours underargon atmosphere. DCM was evacuated by aspirator, and the residue wastreated by MeOH (30 mL) and chloranil (2.10 g, 8.50 mmol), and themixture was stirred at room temperature for 30 min. The mixture wasloaded into a samplet of Biotage, and dried under vacuum. The crudeproduct was purified by chromatography on silica gel column (Biotage,SNAP 340 g, 6.5×18 cm, H₂O:MeCN:HOAc=1:10:0.1˜1:4:0.1) to give Compound(2) (1.60 g, 62%) as dark brown gummy material.

Example 13 Preparation of Compound (21)

A solution of Compound (2) (1.62 g, 2.74 mmol) in MeOH (250 mL) wastreated with 130 mL of 1 M NaOH, and the mixture was stirred at roomtemperature for 2 hours. Acetic acid (35 mL) was added to quench base.The whole mixture was evaporated to obtain 130 mL of crude solution. Thesolution was packed into a column and purified (Biotage C-18 100 g,MeOH:water=0:100˜80:20) to give Compound (21) (788 mg, 56%) as a darkbrown solid.

Example 14 Preparation of Compound (22)

A solution of Compound (21) (10 mg, 0.0194 mmol) and DMAP (3.5 mg,0.0286 mmol) in DMF (2 mL) was treated with Compound (11) (12 mg, 0.0232mmol), and the mixture was stirred at room temperature for 1 hour. DMFwas removed by pump to give a crude product. The product was purified onsilica gel column (Biotage 25 g, 2.5×8 cm, MeOH:CHCl₃=1:3) to giveCompound (22) (4.6 mg, 32%) as a brown solid.

Example 15 Preparation of Compound (24)

A solution of Compound (21) (8 mg, 0.0155 mmol) and DMAP (3.8 mg, 0.031mmol) in DMF (3 mL) was treated with Compound (23) (prepared by themethod described in U.S. Patent Publication No. 2009/0004753, hereinincorporated by reference in its entirety) (16 mg, 0.031 mmol), and themixture was stirred at room temperature for 2 hour. DMF was removed bypump to give a crude product. The product was purified by HPLCchromatography (C-18, H₂O:MeCN=1:10˜1:5) to give Compound (24) (6 mg,52%) as a brown solid.

Example 16 Preparation of Compound (26)

A solution of Compound (21) (8 mg, 0.0155 mmol) and DMAP (3.8 mg, 0.031mmol) in DMF (3 mL) was treated with Compound (25) (prepared by themethod of US 2009/0004753, herein incorporated by reference in itsentirety) (13 mg, 0.031 mmol), and the mixture was stirred at roomtemperature for 2 hour. DMF was removed by pump to give a crude product.The product was purified by chromatography on silica gel column (Biotage25 g, 2.5×8 cm, H₂O:MeCN=1:10˜1:5) to give Compound (26) (5.5 mg, 53%)as a brown solid.

Example 17 Preparation of Compound (25)

A solution of Compound (8) (170 mg, 0.553 mmol) in DMF (5 mL) wastreated with 60% NaH (33.0 mg, 0.825 mmol) and allyl bromide (134 mg,1.11 mmol) at 0° C. The mixture was allowed warm to room temperature andwas stirred overnight (˜16 hours). The reaction was quenched by water(20 mL). The solution was extracted by ethyl acetate (30 mL×3). Thecombined organic layers were washed by water (30 mL×3), brine (50 mL),dried over magnesium sulfate and evaporated to give Compound (25) (210mg, ˜100%) as pale yellow solid. No further purification was required.

Example 18 Preparation of Compound (29)

Compound (25) (210 mg, 0.605 mmol) was treated with anhydrous DCM (8 mL)and Tf₂O (121 μL, 0.719 mmol), and the mixture was stirred at roomtemperature. After 30 min of stiffing, Compound (5) (239 mg, 0.774 mmol)in DCM (6 mL) and DIEA (160 μL, 0.910 mmol) were added. The reaction wasstirred at room temperature for 20 hours. Evaporation gave a crudeproduct. The crude product was purified by chromatography on silica gelcolumn (Biotage, SNAP 50 g, 3.5×8.5 cm, MeOH:CHCl₃=1:10˜1:4) to giveCompound (29) (412 mg, 87%) as a gray gummy material.

Example 19 Preparation of Compound (3)

Compound (29) (390 mg, 0.495 mmol) was treated with MeOH (5 mL) andNaBH₄ (77 mg, 2.04 mmol), and the mixture was stirred at roomtemperature for 30 min. The mixture was evaporated, loaded into a shortsilica gel column (3×5 cm, ethyl acetate:hexanes=1:4) to remove boraneside product. Concentration gave the dihydro-form of Compound (26). Thisintermediate was treated with Pd(PPh₃)₄ (55 mg, 0.0476 mmol),1,3-dimethylbarbituric acid (303 mg, 1.94 mmol) and anhydrous DCM (5mL). The new mixture was cooled in dry ice/acetone bath and evacuatedthrough syringe needle. The flask was filled back with argon andevacuation/refilling with argon was repeated two more times. The mixturewas heated to 40° C. for 16 hours under argon atmosphere. DCM wasevacuated by aspirator, and the residue was treated by MeOH (3 mL) andchloranil (242 mg, 0.984 mmol), and the mixture was stirred at roomtemperature for 30 min. MeOH was removed by aspirator, and the crudeproduct was purified by chromatography on silica gel column (Biotage,SNAP 50 g, 3.5×8.5 cm, MeOH:CHCl₃=1:10˜1:4) to give Compound (3) (135mg, 53%) as dark brown gummy material.

Example 20 Preparation of Compound (27)

A solution of Compound (3) (33 mg, 0.0638 mmol) in MeOH (6 mL) wastreated with 3 mL of 1 M NaOH, and the mixture was stirred at roomtemperature for 2 hours. 1 M HCl (2.8 mL) was added to quench base. Thewhole mixture was evaporated to dryness. The crude product was purifiedby chromatography on silica gel column (Biotage 25 g, 2.5×8 cm,MeOH:CHCl₃=1:3) to give Compound (27) (18 mg, 58%) as a dark brownsolid.

Example 21 Preparation of Compound (28)

A solution of Compound (27) (18 mg, 0.0368 mmol) and DMAP (7.0 mg,0.0573 mmol) in DMF (2 mL) was treated with Compound (11) (26 mg, 0.0442mmol), and the mixture was stirred at room temperature for 1 hour. DMFwas removed by pump to give a crude product. The product was purified bychromatography on silica gel column (Biotage 25 g, 2.5×8 cm,MeOH:CHCl₃=1:3) to give Compound (28) (14 mg, 53%) as a brown solid.

Example 22 Preparation of Compound (30)

A solution of Compound (24, STP ester) (7.0 mg, 0.00940 mmol) andCompound (29) (7 mg, 0.0186 mmol) in DMF (2 mL) was treated with 13 μLof triethylamine (0.094 mmol), and the mixture was stirred at roomtemperature for 1 hour. All volatile materials were removed by vacuumpump overnight. The crude mixture was treated with 1 mL of 1 M TEAAbuffer, and was purified by chromatography on C-18 (Biotage SNAP 12 g,MeOH:H₂O=0:100˜60:40) to give Compound (30) (3.9 mg, 56%) as a darkbrown material.

Example 23 Preparation of Compound (31)

A solution of Compound (29) (80 mg, 0.213 mmol) and Boc₂O (56 mg, 0.255mmol) in DMF (1 mL) was treated with 93 μL of DIEA (0.532 mmol), and themixture was stirred at room temperature. After 5-hour stirring, themixture was treated with bromomethyl acetate (83 μL, 0.848 mmol) andmore DIEA (186 μL, 1.06 mmol), and the mixture was stirred at roomtemperature overnight (>15 hours). All volatile materials were removedby vacuum pump. The residue was dissolved in ethyl acetate (30 mL),washed by water (25 mL), brine (25 mL), and dried over MgSO₄.Evaporation gave the crude product Compound (31) as colorless oil (˜120mg). No further purification was necessary.

Example 24 Preparation of Compound (33)

Compound (31) (20 mg, 0.0346 mmol) was treated with DCM (2 mL) and TFA(0.4 mL), and the mixture was stirred at 0° C. for 1 hour. All volatilematerials were removed by house vacuum and the residue was dried byvacuum pump for 2 hours. The resulting crude amine (Compound (32)) wastreated with Compound (24, STP ester) (10 mg, 0.0134 mmol), DMF (1 mL)and DIEA (12 μL, 0.067 mmol) sequentially. The mixture was stirred atroom temperature for 1 hour. The reaction mixture was dried carefully byvacuum pump, and purified by chromatography on silica gel column(Biotage, SNAP 10 g, MeOH:ethyl acetate:CHCl₃=1:4:4˜1:2:2) to giveCompound (33) (5.1 mg, 31%) as a dark brown material.

Example 25 Preparation of Compound (35)

A solution of Compound (24, STP ester) (10.0 mg, 0.0134 mmol) and DIBOamine (Compound (34), Molecular Probes/C10411) (5.0 mg, 0.0156 mmol) inDMF (1 mL) was treated with 10 μL of triethylamine (0.072 mmol), and themixture was stirred at room temperature for 1 hour. All volatilematerials were removed by vacuum pump overnight. The crude reactionmixture was dried carefully by vacuum pump, and purified bychromatography on silica gel column (Biotage, SNAP 10 g,MeOH:CHCl₃=1:10˜1:6) to give Compound (35) (11.0 mg, 77%) as a darkbrown material.

Example 26 Preparation of EGF Conjugate of Compound (24)

0.6 mg of a 5 mg/ml stock solution of epithelial growth factor (EGF)(120 μL, 0.098 mol) was added into a 2 mL vial. 1.13 mg of Compound (24)STP ester (1.52 μmol) was dissolved in 200 μL of DMSO. 27 μL of thissolution was added into the vial with EGF. The dye to protein molarratio was ˜2. 50 μL of Triethylamine in 0.5 mL of DMSO was dissolved and6 μL of triethylamine solution was added into the EGF solution. Thereaction vessel was covered and stirred for ˜24 hours. The reaction wasquenched with 1.5 M hydroxylamine (pH 8.0) and the mixture was stirredfor ˜30 minutes at room temperature. The conjugate was purified on aP-2F column (15×1 cm) with PBS (pH 7.2). The concentration of theconjugate was measured by determining the A511 nm/A280 nm (60 μg/ml) anddegree of substitution (DOS=1) by absorbance. BSA powder was added tothe conjugate solution (final concentration of 1%) and stirred to gentlydissolve. The EGF conjugate was frozen in dry ice for at least 1 hourand lyophilized for at least 18 hours.

Biological Application Examples of the Fluorescent pH-Sensitive DyeCompounds Example 27 Correlation between pH and Fluorescence of thepH-Sensitive Dye Compounds Provided Herein

The fluorogenic nature of the pH-sensitive fluorescent dye compoundsdescribed herein makes them very useful for studying a variety ofinternalization processes that occur in cells, such as phagocytosis andendocytosis. This is because upon internalization, there is a drop in pHinside the phagosome or endosome which results in an increase offluorescence from the pH-sensitive fluorescent dye compounds.Conjugation of the pH-sensitive fluorescent dye compounds tobiomolecules of interest provide for convenient assays ofinternalization of these molecules. Examples include transferrin, EGFand low-density lipoprotein (LDL) for studying receptor-mediatedendocytosis, and labeled bioparticles, such as E. coli, Staphylococcus,and zymosan for studying phagocytosis. Assays using these fluorogenicbioconjugates offer significant advantages over existing techniques dueto the fact that the pH-sensitive fluorescent dye compounds arerelatively non-fluorescent at the neutral pH outside the cell. Thisreduces or eliminates the need for wash steps and quencher dyes normallyneeded to reduce background signal from bioconjugates outside of thecells.

The study of the fluorescent response of the pH-sensitive fluorescentdye compounds to changes in pH was performed in aqueous buffers (inconcentrations around 10 μmol/mL). The results of the titrations areshown in FIGS. 3-5.

Example 28 Intracellular Uptake of the Fluorescent pH-Sensitive DyeCompounds

FIG. 2, panel B shows cellular internalization of an exemplarypH-sensitive fluorescent dye compound. Cells were imaged using standardfluorescent illumination and microscopy.

RAW macrophage cells were plated onto poly-D-lysine coated glass dishesand cultured under normal conditions. To demonstrate phagocytic uptakeof the fluorescent pH-sensitive dye compound (Compound (1))-labeled E.coli, Staphylococcus and zymosan (yeast) bioparticles, culture mediumwas removed and the cells were washed in pH-neutral buffer before thelabeled bioparticles were added. Cells were incubated for 90 minutes at37 ° C. and imaged with a standard FITC filter set (see, FIG. 6).

FIG. 7 shows a dose-response curve of cytochalasin D inhibition ofCompound (1)-labeled bioparticle internalization in a high-throughputmicroplate-based assay. These results demonstrated that an extracellularquenching agent “BackDrop” had a minimal effect on the magnitude ofspecific internalization and background fluorescence in the assay, whichmay be carried out with no washes or extracellular quenching to achievea physiologically relevant and functional measurement of the phagocyticindex of cultured macrophage “MMM” cells.

FIG. 8A shows a series of pH curves for E. coli bioparticles labeledwith Compound (2), Compound (12) and Compound (28), emphasizing theirrelative responses to acidification in vitro. Briefly, E. coli labeledwith the indicated dye species were resuspended at 100 μg/mL at pH 4pH-8.5. 100 mL of the suspension was dispensed into a 96-well plate forimaging on a Hamamatsu FDSS 6000 and the wells were imaged with standardFITC illumination. The fluorescence range is pseudocolored red forbrightest signal (acidic pH) to blue (for alkaline pH) (see, FIG. 8B).

In FIG. 9, 10,000 MW dextran was labeled with Compound (22) andresuspended at 1 μg/mL in aqueous solution, buffered to the pH indicatedon the plot. Samples were placed in a fluorimeter and excited at 488 nm,while scanning emission across the wavelengths shown. Plots show therelative fluorescence increase with acidification.

Example 29 Reaction of Goat Anti-Mouse IgG (GAM) and Compound (24)

0.100 mL (1.0 mg) of a 10.0 mg/mL solution of GAM in 10 mM potassiumphosphate, 150 mM sodium chloride buffer (PBS) was measured intoreaction tubes and the pH raised to >8.0 with 10 μL 1 M sodiumbicarbonate, pH 9.0. The GAM solution was reacted with a 2.5, 5, 10, 15,or 20-fold molar excess of Compound (24) at 10 mg/mL in anhydrous DMSOfor 1 h at room temperature. The dye-protein conjugates were separatedfrom free dye by size exclusion chromatography using 5-0.75×20 cmcolumns packed with BioRad™ Bio-Gel® P-30 fine in PBS and eluted withsame. The initial protein-containing band from each column wascollected. Absorbance spectra were obtained on a Perkin-Elmer Lambda 35UV/Vis spectrometer, diluting the samples in guanidine-HCL. The degreeof substitution (DOS) measured ranged from 0.8-3.2 respectively.

Example 30 Antibody Labeling using pH-Sensitive Fluorescent DyeCompounds

A freshly prepared 10 mM DMSO solution of Thiol reactive Compound(24)-maleimide conjugate was added to an IgG solution (6 mg/mL) in PBSbuffer at pH 7.0-7.5 in sufficient amount to give 10-20 moles of dye foreach IgG molecule. The reaction was allowed to proceed for approximately2 hours at which time the reaction mixture was poured on to a pre-packedSephadex G-25 column. The column was eluted with PBS buffer to collectpurified conjugated IgG. TLC analysis of a small aliquot (˜5 μL) of thepurified IgG indicated no free dye in the conjugate solution. The degreeof labeling (DOL) was determined through a typical absorbance reading.

TABLE 4 Compound (24)-labeled IgG Properties Compound Moles of dye/IgGmolecule Observed DOL 24 10 2 24 20 1.8

Labeled IgGs were collected from the column and checked for purity viathin layer chromatography, to insure that all free dye was separatedfrom the labeled IgG. These samples were diluted 1:10 to finalconcentrations of 10-100 μg/mL into a series of pH standard solutionsfrom pH 4 to pH 9 and transferred into a 96 well microplate and scannedfor fluorescence in a Molecular Devices FlexStation 384 plate reader. Ascan be seen in FIG. 10, relative fluorescence units (RFU) on the y-axisdemonstrate the pH activation of fluorescent signal from the IgGconjugates, increasing signal with decreasing pH. pKa (midpoint) valuesnear 6.8 of the conjugated antibodies track closely with the signal fromthe pH-sensitive fluorescent dyes.

Example 31 Reaction of Fab Fragment of Goat Anti-Human IgG (GAH) andCompound (24)

0.123 mL (1.0 mg) of an 8.18 mg/mL solution of GAH in 10 mM potassiumphosphate, 150 mM sodium chloride buffer (PBS) was measured into areaction tube and the pH raised to >8.0 with 12.5 μL 1 M sodiumbicarbonate, pH 9.0. The GAH solution was reacted with a 12-fold molarexcess of Compound (24) at 10 mg/mL in anhydrous DMSO for 1 h at roomtemperature. The dye-protein conjugate was separated from free dye bysize exclusion chromatography using a 0.75×20 cm column packed withBioRad™ Bio-Gel® P-30 fine in PBS and eluted with same. The initialprotein-containing band from the column was collected. The absorbancespectrum was obtained on a Perkin-Elmer Lambda 35 UV/Vis spectrometer,diluting the sample in guanidine-HCL. The degree of substitution (DOS)measured was 1.4. The fluorescence emission spectra were obtained usinga Perkin-Elmer LS 55Fluorescence Spectrometer, excited at 475 nm. FIG.11 shows a pH response Compound (24)-labeled goat-anti-human (GAH) Fabfragment. The solid line shows the pH response at pH 10, the diamondline shows the pH response at pH 8, the triangle line shows the pHresponse at pH 6, and the square line shows the pH response at pH 4.

Example 32 Live Cell Phagocytosis/Endocytosis with Dye Conjugates

A 431 cells were grown in complete medium on 35 mm poly-D-lysine coatedglass bottom culture dishes from MatTek. On the day of the assay, cellswere rinsed once with LCIS+1% BSA (Live Cell imaging solution,Cat#A14291DJ) and placed at 37° C. Control dishes received LCIS; EGFpretreatment dishes received 10 μg/mL unlabeled EGF in LCIS. Cells wereincubated at 37° C. for 30 minutes. Cells were then cooled to 4° C. onice for 10 minutes. Compound (24)-labeled EGF was added to the dishes1:10 at 5 μg/mL from a 50 μg/mL stock in LCIS. These dishes wereincubated on ice for 30 minutes, then washed 2× with cold LCIS andallowed to warm to 37° C. for 60 minutes before imaging with standardTRITC and FITC filter sets on a DeltaVision Core microscope. Cellspretreated with unlabeled EGF showed no signal owing to the occlusion ofdye-labeled EGF binding sites and internalization of EGF receptors byexcess unlabeled EGF. Specific signal from untreated plates was fromdye-labeled EGF internalization. All images were matched for gain andexposure times. FIG. 12 shows internalization of EGF conjugated toCompound (24). The left panel shows cells pretreated with EGF and theright panel shows cells treated with dye-conjugated EGF.

pH-sensitive fluorescent dye compounds were made up in LCIS from 5 and10 mM DMSO stocks respectively, and loaded for imaging as follows:

10 mL loading buffer, Compound (33): 10 μL Compound (33) from a 10 mMDMSO stock was added to 100 μL Powerload and mixed. 10 mL LCIS was addedto this solution for final concentration of dye compound-AM ester of 10μM.

Cells were cultured on 35 mm MatTek glass bottom dishes. For loading,cells were rinsed 1× with LCIS and replaced with loading bufferdescribed above. Cells were incubated at 37° C. for 60 minutes, thenrinsed 2× with LCIS and imaged with standard TRITC or FITC filter sets.(see FIG. 13).

Example 33 Labeling of Transferrin with pH Sensing Dyes

All materials are from Life Technologies Corp. (Carlsbad, Calif.) unlessotherwise stated. Dissolve transferrin from human serum (Sigma, T4132)in 0.1 M NaHCO₃, pH 8.3, to a concentration of 10 mg/mL. Make a 10 mg/mLsolution of the succinimidyl ester of the dye in dry DMSO and sonicatebriefly to aid in dissolution of the dye. Add a 10 to 30-fold molarexcess of the reactive dye solution to the transferrin solution dropwisewhile stiffing. Note that the volume of dye added depends on thespecific dye and the amount of transferrin to be labeled. Protect thereaction vessel from light and stir for ˜1 hour at room temperature.Purify the conjugate on a P-30M gel filtration column (BioRad, 150-4150)in PBS, pH 7.2. Centrifuge the conjugate at 19,000 rpm for 20 minutes toremove aggregates, if present. Determine the degree of labeling bymeasuring A560 nm/A280 nm.

Example 34 Monitoring Cytosolic Acidification Associated with IonChannel or Transporter Activation

A cytosolically localized version of the pH-sensitive fluorescent dyecompound is be a useful indication of proton influx through ion channelsor transporters. This may be used for screening of antagonists,agonists, and other modulators of channel/transporter function.

Example 35 Receptor Internalization Assay

The β-2-Adrenergic Receptor (β2AR) is modified to incorporate an epitopetag (VSV-G tag) at the N-terminus. A clonal, stable HEK 293 cell line isestablished which expresses this receptor (approximately 1.8 pmol/mgcell homogenate). Anti-VSV-G antibody labeled with a pH-sensitivefluorescent dye compound described herein is used to monitoragonist-mediated receptor internalization in these live cells. The assayis performed in the presence and absence of a specific agonist,isoproterenol.

a) Isoproterenol-induced receptor internalization in VSV-G-B2 Adrenergiccells. For HEK 293 cells it is preferable to coat plates withpoly-D-lysine (Sigma P-6407, 5 mg in 50 ml sterile PBS) prior to seedingthe cells. 30-80 μl/well is added and maintained at room temperature for45 minutes. The coating solution is then aspirated, washed 4× (or more)with 100 μl sterile PBS. Plates can be treated in advance and stored at4° C. for up to a week (with the final PBS wash still in the wells).Cultured cells can be seeded directly into the wells without firstdrying the plates. Cultured cells are diluted to ˜1.6×105 cells/ml incomplete MEM media (Sigma M2279) containing 200 μg/ml G418. 100 μl ofcell suspension is pipetted into each assay well of a poly-D-lysinetreated 96-well Packard Viewplate (cell density=16000 cells per well).Plates are then incubated 24-48 hours at 37° C. with 5% CO₂. 250 μglyophilized dye compound-labeled anti-VSV-G antibody (PA45407) isreconstituted with 0.5 ml sterile deionized water and mixed thoroughly(stock concentration 0.5 mg/ml). The mixture is centrifuged to removeany precipitate. The dye compound-labeled anti-VSV-G antibody is furtherdiluted to a concentration of 2.5-5 μg/ml using serum-free, phenol redfree MEM media. Hoechst 33342 nuclear stain may be added to the 2.5-5μg/ml antibody solution to a final concentration of 5 μM. Media issubsequently removed from the cells and 100 μl antibody and Hoechstsolution is added to each well. The solution is then incubated at roomtemperature for 15 minutes. 3 μM working dilution of isoproterenolagonist (from 10mM stock in sterile water; Sigma 15627) is added to thesolution and then 50 μl is added to required wells, giving 1 μM finalconcentration. The wells are incubated at 37° C. for 30 minutes (in aCO₂ incubator or on the IN Cell Analyzer 3000). The cells are imaged onan IN Cell Analyzer 3000, IN Cell Analyzer 1000 or a confocalmicroscope.

b) Internalization of Compound-labeled anti-VSV-G antibody. HEK 293cells expressing a VSV-G-(2-Adrenergic Receptor are preincubated withanti-VSV-G antibody-dye compound conjugate and stimulated with 1 μMisoproterenol. The cells are imaged using an IN Cell Analyzer 1000.Quantification of the agonist-mediated response is achieved using agranularity algorithm, which defines grains as distinct focal regionswithin a cell that have pronounced intensity differences from the regionof the cell immediately surrounding the grains. The operator can adjusta variety of parameters to control what size and intensity of grain willbe counted and analyzed.

c) Internalization of Compound-labeled anti-VSV-G antibody. HEKVSV-G-β2-Adrenergic Receptor cells are preincubated with compoundlabeled anti-VSV-G antibody and increasing concentrations ofisoproterenol (0-1 μM) are then added to the cells. After 30 minutes at37° C., agonist mediated internalization is analyzed by measuring theincrease in compound fluorescence using an IN Cell Analyzer 1000 and thegranularity analysis algorithm.

Example 36 Detection of Neuronal Cells with a pH-Sensitive FluorescentDye Compound

Astroglial feeder layers are established for one week in culture onglass bottomed culture dishes, 35 mm diameter, coated withpoly-L-lysine. Neurons from embryonic day 18 rat hippocampi aredissociated in culture medium, and seeded onto the feeder layers at adensity of 25-35,000 cells per milliliter, two milliliters per dish, andallowed to grow in neuronal culture medium plus mitotic inhibitors toprevent glial proliferation.

Cells are pre-stained for 15 minutes with 200 ng/mL Hoescht to visualizeDNA in the nuclei, and 50 ng/mL calcien AM ester to visualize cytoplasmby adding 1000× DMSO stocks of these compounds to the cells in completemedium, and then returning them to the cell culture incubator forfifteen minutes at 37° C. Cells are removed, and the medium is gentlypoured off. The cells are immediately placed in 5 μM pH-sensitivefluorescent dye compound, diluted from a 1 mM DMSO stock into normalsaline plus 20 mM HEPES and 20 mM glucose, final pH set to 7.4 withNaOH. The cells are incubated in labeling solution for ten minutes atroom temperature, and then gently washed twice with saline (above) minusdye for imaging.

Example 37 Phagocytosis of β1 Amyloid Conjugates

1 mg of beta amyloid 1-42 is labeled with a pH-sensitive fluorescent dyecompound to yield a dye-beta amyloid conjugate, which is purified by gelfiltration to yield a solution of approximately 200 ng/mL with a degreeof labeling between 1 and 2 dye molecules per beta amyloid molecule.

2 mL of J774A.1 cells are seeded onto 35 mm, poly-D-lysine coated glassbottom culture dishes at a density of 35,000 cells per mL one day inadvance of the study, in serum-free OptiMem culture medium. The dye-betaamyloid conjugate is filtered through a 0.2 micron syringe filter, and20 microliters of the solution is added to the cells. The culture isreturned to the incubator (37° C., 5% CO₂) for overnight incubation, andimaged on the following day.

Example 38 Copper-Less Click Reactions using DIBO-ContainingpH-Sensitive Fluorescent Dye Compounds

a) Live Cell Labeling: Mammalian cells are grown in an appropriatemedium at 37° C. in 5% CO₂. Supplement the growth medium with anazide-derivatized metabolite (e.g., Click-iT® ManNAz, Life Technologies,Catalog No. C33366) and grow the cells for 2 to 3 days. Wash the cellstwo times with D-PBS (Life Technologies, Catalog No. 14190-144)containing 1% fetal bovine serum (FBS). Label the azide-modifiedmacromolecules at room temperature in the dark for 1 hour with about 5to 30 μM Compound (35) in D-PBS containing 1% FBS. Wash the cells fourtimes with D-PBS containing 1% FBS. Fix the cells with 4% formaldehydein D-PBS for 15 minutes at room temperature. Wash the cells with D-PBS.Optionally, counterstain the cells with an appropriate counterstain,such as Hoechst 33342 and wash the cells. Image the cells.

b) Protein Labeling: Introduce azide into proteins, e.g., using GalNAzin antibodies using the Click-iT® O-GlcNAc Enzymatic Labeling System(Life Technologies, Catalog No. C33368). Modify the protein-bound azidewith Compound (35). Incubate the protein in TBS with about 5 to 10 μMCompound (35) for at least 1 hour at room temperature. Remove the excesslabel. Analyze the modified protein.

1. A pH-sensitive fluorescent dye compound of structural formula (I):

wherein R¹ is alkoxy or thioalkyl; R² and R⁶, which may be the same ordifferent, are each independently H, halogen, —OR^(a), —SR^(a),—NR^(a)R^(b), or an electron donating group; R³ is —NR′R″, wherein R′and R″, which may be the same or different, are each independently alkylor substituted alkyl; R⁴ is selected from the group consisting of alkyland substituted alkyl; R⁵ is selected from the group consisting ofalkyl; substituted alkyl; alkenyl; substituted alkenyl; acyl; aryl;substituted aryl; carboxyalkyl; heteroaryl; substituted heteroaryl;heterocyclyl; substituted heterocyclyl; alkylcarboxy;alkylalkoxycarbonyl; alkylaminocarbonyl; alkylaryloxycarbonyl;alkylheteroaryl; (CH₂),_(n)CO(O)R; (CH₂),_(n)C(O)R; (CH₂)_(n)C(O)NHR;(CH₂)_(n)C(O)NRR^(c); wherein n is an integer from 1 to 6, and R andR^(c), which may be the same or different, are each independently H,alkyl, substituted alkyl, aryl, substituted aryl, heteroaryl,substituted heteroaryl, substituted amino, alkylaminocarbonyl,aminodextran, amide, a protein, a lipophilic group, or R^(d), whereinR^(d) is (CH₂)_(n)C(O)NHR, wherein n is an integer from 1 to 6, andR_(x) is a reactive group; -L-R_(x); and -L-S_(c), wherein L is alinker, R_(x) is a reactive group, and S, is a conjugated substance;R^(a) is H, alkyl, or substituted alkyl; and R^(b) is alkyl orsubstituted alkyl.
 2. The compound according to claim 1, wherein R¹ isalkoxy or thioalkyl; R² and R⁶, which may be the same or different, areeach independently H or halogen; R³ is —NR′R″, wherein R′ and R″, whichmay be the same or different, are each independently alkyl; R⁴ is alkyl;and R⁵ is selected from the group consisting of alkyl; substitutedalkyl; alkenyl; substituted alkenyl; acyl; aryl; substituted aryl;carboxyalkyl; heteroaryl; substituted heteroaryl; heterocyclyl;substituted heterocyclyl; alkylcarboxy; alkylalkoxycarbonyl;alkylaminocarbonyl; alkylaryloxycarbonyl; alkylheteroaryl;(CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NRR^(c);wherein n is an integer from 1 to 6, and R and R^(c), which may be thesame or different, are each independently H, alkyl, substituted alkyl,aryl, substituted aryl, heteroaryl, substituted heteroaryl, substitutedamino, alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilicgroup, or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is aninteger from 1 to 6, and R_(x) is a reactive group; -L-R_(x); and-L-S_(c).
 3. The compound according to claim 1, wherein R¹ is alkoxy orthioalkyl; R² and R⁶, which may be the same or different, are eachindependently H, Cl or F; R³ is —NR′R″, wherein R′ and R″, which may bethe same or different, are each independently alkyl; R⁴ is alkyl; and R⁵is selected from the group consisting of alkyl; substituted alkyl;alkenyl; substituted alkenyl; acyl; aryl; substituted aryl;carboxyalkyl; heteroaryl; substituted heteroaryl; heterocyclyl;substituted heterocyclyl; alkylcarboxy; alkylalkoxycarbonyl;alkylaminocarbonyl; alkylaryloxycarbonyl; alkylheteroaryl;(CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NRR^(c);wherein n is an integer from 1 to 6, and R and R^(c), which may be thesame or different, are each independently H, alkyl, substituted alkyl,aryl, substituted aryl, heteroaryl, substituted heteroaryl, substitutedamino, alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilicgroup, or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is aninteger from 1 to 6, and R_(x) is a reactive group; -L-R_(x); and-L-S_(c).
 4. The compound according to claim 1, wherein R¹ is alkoxy orthioalkyl; R² and R⁶ are each H; R³ is —NR′R″, wherein R′ and R″, whichmay be the same or different, are each independently alkyl; R⁴ is alkyl;and R⁵ is selected from the group consisting of alkyl; substitutedalkyl; alkenyl; substituted alkenyl; acyl; aryl; substituted aryl;carboxyalkyl; heteroaryl; substituted heteroaryl; heterocyclyl;substituted heterocyclyl; alkylcarboxy; alkylalkoxycarbonyl;alkylaminocarbonyl; alkylaryloxycarbonyl; alkylheteroaryl;(CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NRR^(c);wherein n is an integer from 1 to 6, and R and R^(c), which may be thesame or different, are each independently H, alkyl, substituted alkyl,aryl, substituted aryl, heteroaryl, substituted heteroaryl, substitutedamino, alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilicgroup, or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is aninteger from 1 to 6, and R_(x) is a reactive group; -L-R_(x); and-L-S_(c).
 5. The compound according to claim 1, wherein R¹ is methoxy;R² and R⁶ are each H; R³ is —NR′R″, wherein R′ and R″, which may be thesame or different, are each independently methyl or ethyl; R⁴ is methylor ethyl; R⁵ is methyl; ethyl; carboxyalkyl; (CH₂)_(n)CO(O)R;(CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NRR^(c); wherein n is aninteger from 1 to 6, and R and R^(c), which may be the same ordifferent, are each independently H, alkyl, substituted alkyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, substituted amino,alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilic group,or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is an integerfrom 1 to 6, and R_(x) is a reactive group selected from carboxyl,carboxylester, amide, maleimide, succinimidyl ester (SE),sulfodichlorophenol (SDP) ester, sulfotetrafluorophenol (STP) ester,tetrafluorophenol (TFP) ester, acetoxymethoxy (AM) ester,nitrilotriacetic acid (NTA), aminodextran, DIBO-amine; -L-R_(x); or-L-S_(c).
 6. A pH-sensitive fluorescent dye compound of structuralformula (II):

wherein R¹ is alkoxy or thioalkyl; R² and R⁶, which may be the same ordifferent, are each independently H, halogen, —OR^(a), —SR^(a),—NR^(a)R^(b), or an electron donating group; R³ is —NR′R″, wherein R′and R″, which may be the same or different, are each independently alkylor substituted alkyl; R⁴ is selected from the group consisting of alkyland substituted alkyl; R⁵ is selected from the group consisting ofalkyl; substituted alkyl; alkenyl; substituted alkenyl; acyl; aryl;substituted aryl; carboxyalkyl; heteroaryl; substituted heteroaryl;heterocyclyl; substituted heterocyclyl; alkylcarboxy;alkylalkoxycarbonyl; alkylaminocarbonyl; alkylaryloxycarbonyl;alkylheteroaryl; (CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR;(CH₂)_(n)C(O)NRR^(c); wherein n is an integer from 1 to 6, and R andR^(c), which may be the same or different, are each independently H,alkyl, substituted alkyl, aryl, substituted aryl, heteroaryl,substituted heteroaryl, substituted amino, alkylaminocarbonyl,aminodextran, amide, a protein, a lipophilic group, or R^(d), whereinR^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is an integer from 1 to 6, andR_(x) is a reactive group; -L-R_(x); and -L-S_(c), wherein L is alinker, R_(x) is a reactive group, and S, is a conjugated substance;R^(a) is H, alkyl, or substituted alkyl; and R^(b) is alkyl orsubstituted alkyl.
 7. The compound according to claim 6, wherein R¹ isalkoxy or thioalkyl; R² and R⁶, which may be the same or different, areeach independently H or halogen; R³ is —NR′R″, wherein R′ and R″, whichmay be the same or different, are each independently alkyl; R⁴ is alkyl;and R⁵ is selected from the group consisting of alkyl; substitutedalkyl; alkenyl; substituted alkenyl; acyl; aryl; substituted aryl;carboxyalkyl; heteroaryl; substituted heteroaryl; heterocyclyl;substituted heterocyclyl; alkylcarboxy; alkylalkoxycarbonyl;alkylaminocarbonyl; alkylaryloxycarbonyl; alkylheteroaryl;(CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NRR^(c);wherein n is an integer from 1 to 6, and R and R^(c), which may be thesame or different, are each independently H, alkyl, substituted alkyl,aryl, substituted aryl, heteroaryl, substituted heteroaryl, substitutedamino, alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilicgroup, or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is aninteger from 1 to 6, and R_(x) is a reactive group; -L-R_(x); and-L-S_(c).
 8. The compound according to claim 6, wherein R¹ is alkoxy orthioalkyl; R² and R⁶, which may be the same or different, are eachindependently H, Cl or F; R³ is —NR′R″, wherein R′ and R″, which may bethe same or different, are each independently alkyl; R⁴ is alkyl; and R⁵is selected from the group consisting of alkyl; substituted alkyl;alkenyl; substituted alkenyl; acyl; aryl; substituted aryl;carboxyalkyl; heteroaryl; substituted heteroaryl; heterocyclyl;substituted heterocyclyl; alkylcarboxy; alkylalkoxycarbonyl;alkylaminocarbonyl; alkylaryloxycarbonyl; alkylheteroaryl;(CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NRR^(c);wherein n is an integer from 1 to 6, and R and R^(c), which may be thesame or different, are each independently H, alkyl, substituted alkyl,aryl, substituted aryl, heteroaryl, substituted heteroaryl, substitutedamino, alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilicgroup, or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is aninteger from 1 to 6, and R_(x) is a reactive group; -L-R_(x); and-L-S_(c).
 9. The compound according to claim 6, wherein R¹ is alkoxy orthioalkyl; R² and R⁶ are each H; R³ is —NR′R″, wherein R′ and R″, whichmay be the same or different, are each independently alkyl; R⁴ is alkyl;and R⁵ is selected from the group consisting of alkyl; substitutedalkyl; alkenyl; substituted alkenyl; acyl; aryl; substituted aryl;carboxyalkyl; heteroaryl; substituted heteroaryl; heterocyclyl;substituted heterocyclyl; alkylcarboxy; alkylalkoxycarbonyl;alkylaminocarbonyl; alkylaryloxycarbonyl; alkylheteroaryl;(CH₂)_(n)CO(O)R; (CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NRR^(c);wherein n is an integer from 1 to 6, and R and R^(c), which may be thesame or different, are each independently H, alkyl, substituted alkyl,aryl, substituted aryl, heteroaryl, substituted heteroaryl, substitutedamino, alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilicgroup, or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is aninteger from 1 to 6, and R_(x) is a reactive group; -L-R_(x); and-L-S_(c).
 10. The compound according to claim 6, wherein R¹ is methoxy;R² and R⁶ are each H; R³ is —NR′R″, wherein R′ and R″, which may be thesame or different, are each independently methyl or ethyl; R⁴ is methylor ethyl; and R⁵ is methyl; ethyl; carboxyalkyl; (CH₂)_(n)CO(O)R;(CH₂)_(n)C(O)R; (CH₂)_(n)C(O)NHR; (CH₂)_(n)C(O)NRR^(c); wherein n is aninteger from 1 to 6, and R and R^(c), which may be the same ordifferent, are each independently H, alkyl, substituted alkyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, substituted amino,alkylaminocarbonyl, aminodextran, amide, a protein, a lipophilic group,or R^(d), wherein R^(d) is (CH₂)_(n)C(O)NHR_(x), wherein n is an integerfrom 1 to 6, and R_(x) is a reactive group selected from carboxyl,carboxylester, amide, maleimide, succinimidyl ester (SE),sulfodichlorophenol (SDP) ester, sulfotetrafluorophenol (STP) ester,tetrafluorophenol (TFP) ester, acetoxymethoxy (AM) ester,nitrilotriacetic acid (NTA), aminodextran, DIBO-amine; -L-R_(x); or-L-S_(c).
 11. A pH-sensitive dye compound selected from the groupconsisting of:


12. A composition for determining the pH of a sample, the compositioncomprising: a) one or more of the pH-sensitive fluorescent dye compoundsaccording to claim 1; and b) a carrier, wherein the one or morepH-sensitive fluorescent dye compounds are present in an amounteffective to detect the pH of the sample.
 13. A composition fordetermining the pH of a sample, the composition comprising: (a) one ormore of the pH-sensitive fluorescent dye compounds according claim 1;and (b) an analyte, wherein the one or more pH-sensitive fluorescent dyecompounds are present in an amount effective to detect the pH of thesample.
 14. A method for determining the pH of a sample, the methodcomprising: (a) contacting the sample with one or more of thepH-sensitive fluorescent dye compounds according to claim 1 to form acontacted sample; (b) incubating the contacted sample for an appropriateamount of time to form an incubated sample; (c) illuminating theincubated sample with an appropriate wavelength to form an illuminatedsample; and (d) detecting fluorescent emissions from the illuminatedsample; wherein the fluorescent emissions are used to determine the pHof the sample.
 15. (canceled)
 16. A method for monitoring the pH insidea live cell, the method comprising: (a) contacting the cell with one ormore of the pH-sensitive fluorescent dye compounds according to claim 1to form a contacted cell; (b) incubating the contacted cell for asufficient amount of time for the one or more of the dye compounds orcompositions to enter the cell to form a labeled cell; (c) illuminatingthe labeled cell with an appropriate wavelength to form an illuminatedcell; and (d) detecting fluorescent emissions from the illuminated cell;wherein the fluorescent emissions are used to monitor the pH inside thecell.
 17. (canceled)
 18. A method for detecting phagocytosis of acarrier molecule in solution, the method comprising: (a) conjugating thecarrier molecule to one or more of the pH-sensitive fluorescent dyecompounds according to claim 1 to form a carrier conjugate; (b)contacting the carrier conjugate with a cell to form a contacted cell;(c) incubating the contacted cell to form an incubated solution; (d)illuminating the incubated solution to form an illuminated solution; and(e) detecting fluorescent emissions from the illuminated solution;wherein fluorescent emissions indicate phagocytosis of the carriermolecule.
 19. (canceled)
 20. A method for detecting a pH relatedintracellular process, the method comprising: (a) contacting one or moreof the pH-sensitive fluorescent dye compounds according to claim 1 witha cell to form a contacted cell; (b) incubating the contacted cell toform an incubated solution; (c) illuminating the incubated solution toform an illuminated solution; and (d) detecting fluorescent emissionsfrom the illuminated solution; wherein increased fluorescent emissionsindicates activation of the intracellular process.
 21. (canceled)
 22. Amethod for identifying a target cell in a population of cells, whereinthe target cell is differentially labeled relative to neighboring cellswithin the population, the method comprising: (a) contacting one or moreof the pH-sensitive dye compounds according to claim 1 with thepopulation of cells to form a contacted cell population; (b) incubatingthe contacted cell population for a period of time sufficient for theone or more of the pH-sensitive dye compounds to enter the target cell,thereby forming an incubated cell population; and (c) illuminating theincubated cell population, wherein the target cell is identified by adifferential label relative to neighboring cells within the population.23. (canceled)
 24. A method for diagnosing or detecting a disease in asubject, the method comprising: (a) contacting a sample obtained from asubject suspected of having the disease with one or more of thepH-sensitive dye compounds according to claim 1 to form a contactedsample; (b) incubating the contacted sample for an appropriate amount oftime to form an incubated sample; (c) illuminating the incubated samplewith an appropriate wavelength to form an illuminated sample; and (d)detecting fluorescent emissions from the illuminated sample; wherein thefluorescent emissions are used to diagnose or detect the disease. 25-26.(canceled)
 27. A kit for determining the pH of a sample comprising: (a)one or more of the pH-sensitive dye compounds according to claim 1; (b)one or more containers; and optionally (c) instructions for determiningthe pH of the sample. 28-30. (canceled)